Methods and compositions for producing solvents

ABSTRACT

Described herein are methods, compositions and synthetic biology approaches for solvent production, including but not limited to butanol production. Described herein are recombinant bacteria and yeast strains which may be used in production of a solvent, including but not limited to butanol, from lignocellulosic and other plant-based feedstocks. Described herein are methods of producing solvents, including but not limited to butanol, using bacteria and yeast strains. Described herein are methods of producing organisms that display highly efficient butanol production.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of priority to U.S. ProvisionalApplication Ser. No. 60/930,775, filed May 17, 2007 the contents ofwhich are incorporated by reference herein in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with United States Government support under USAgrant number 2001-35504-10668. The Government may retain certain rightsin the invention.

FIELD OF INVENTION

The compositions and methods described herein pertain to the generationof solvents, including but not limited to the generation of butanol.Specifically, the invention relates to genetic modification ofsolventogenic microorganisms to enhance production of solvents. Morespecifically, the invention relates to genetic modification ofsolventogenic clostridia to enhance efficiency of production of butanol.

BACKGROUND OF THE INVENTION

With the inevitable depletion of petroleum reserves, fast-growing globalpopulations, and widespread industrialization, there has been anincreasing worldwide interest in renewable energies. There is a growingconsensus that producing liquid biofuels such as ethanol from renewableand inexpensive lignocellulosic-based plant materials (biomass) has agreat potential to meet a large portion of this nation's energy demandin the transportation sector. Moreover, producing biofuels from biomasswill simultaneously address three important societal concerns: securityof supply (biofuels can be produced locally in sustainable systems),lower greenhouse gas (biofuels recycle carbon dioxide), and support ofagriculture. The U.S. Department of Energy (DOE) has set a goal toreplace 30% of the liquid transportation fuel with biofuels by 2030.

Similar to ethanol, butanol has many favorable attributes as a fuelmolecule. However, it is an underexploited biofuel. Butanol can beproduced as a co-product with ethanol and acetone from carbohydratesthrough fermentation by several solventogenic Clostridia. Compared tothe currently popular fuel additive, ethanol, butanol has severaladvantages. It contains around 22% oxygen which when used as a fuel willresult in more complete combustion and low exhaust smoke. In addition,it has a higher energy content (BTU/volume) than ethanol, is moremiscible with gasoline and diesel, and has a lower vapor pressure andsolubility characteristics which would allow for it to be shipped bypipeline, unlike ethanol.

Solventogenic clostridia are well-known as natural producers of organicsolvents via fermentation process. C. acetobutylicum and C. beijerinckiiare among the prominent solvent-producing strains capable of producingacetone and butanol as the main fermentation products (Jones, D. T., andD. R. Woods. 1986. Acetone-butanol fermentation revisited. Microbiol.Mol. Biol. Rev. 50: 484-524.) Efforts have been made to improve theClostridia-based butanol fermentation processes by developing newstrains and downstream technologies. For example, as described in U.S.Pat. No. 6,358,717, which is incorporated herein by reference in itsentirety, Blaschek and others used chemical mutagenesis to develop amutant strain of Clostridium beijerinckii, BA101 with higher butanolconcentration. To circumvent butanol inhibition, Blaschek and othersalso developed various downstream processes including gas stripping,pervaporation, and liquid-liquid extraction. See, e.g., Ezeji, T. C.,Qureshi, N. & Blaschek, H. P. Butanol fermentation research: Upstreamand downstream manipulations. Chem Rec 4, 305-314 (2004); US Pat. Pub.No. 2005/0089979; Qureshi et al., Butanol production using Clostridiumbeijerinckii BA101 hyper-butanol producing mutant strain and recovery bypervaporation, Appl Biochem Biotech 84-6, 225-235 (2000); Formanek etal., Enhanced butanol production by Clostridium beijerinckii BA101 grownin semidefined P2 medium containing 6 percent maltodextrin or glucose.Applied and Env. Microbiol. 63(6):2306-2310 (1997); and Ezeji et al.,Acetone butanol ethanol (ABE) production from concentrated substrate:reduction in substrate inhibition by fed-batch technique and productinhibition by gas stripping, Appl Microbiol Biot 63, 653-658 (2004),each of which is incorporated herein by reference in its entirety.

The butanol biosynthesis pathway of the solvent producing Clostridia hasbeen studied, and some of the enzymes involved therein have beenpurified and characterized. See, e.g., Boynton et al., Cloning,sequencing, and expression of clustered genes encodingbeta-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, andbutyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824,Journal of Bacteriology 178, 3015-3024 (1996); Petersen & Bennett,Cloning of the Clostridium acetobutylicum ATCC 824 Acetyl Coenzyme-aAcetyltransferase (Thiolase-Ec 2.3.1.9) Gene, Applied and EnvironmentalMicrobiology 57, 2735-2741 (1991); Petersen et al., Molecular-Cloning ofan Alcohol (Butanol) Dehydrogenase Gene-Cluster from Clostridiumacetobutylicum ATCC-824, Journal of Bacteriology 173, 1831-1834 (1991);and Durre et al., Solventogenic Enzymes of Clostridiumacetobutylicum—Catalytic Properties, Genetic Organization, andTranscriptional Regulation, Fems Microbiol Rev 17, 251-262 (1995), eachof which is incorporated herein by reference in its entirety.

Butanol fermentation has traditionally been constrained byself-limitation of the reaction due to the toxic effect of the producton the microorganism involved in the process. There is a need forproducing solventogenic microorganisms such as clostridia that achieveincreased efficiency in the production of bio-butanol.

BRIEF SUMMARY OF THE INVENTION

Described herein are methods, systems and synthetic biology approachesfor solvent production, including but not limited to butanol production.Described herein are recombinant bacteria and yeast strains which may beused in production of butanol from lignocellulosic and other plant-basedfeedstocks. Described herein are methods of producing solvents,including but not limited to butanol, using recombinant bacteria andyeast strains.

Described herein are genetically-modified solventogenic organism strainscomprising altered expression or structure of a gene relative to theoriginal organism strain, wherein such genetic modifications result inincreased efficiency of solvent production. Described herein aregenetically-modified solventogenic clostridia strains comprising alteredexpression or structure of a gene relative to the clostridia strainprior to its genetic modification, wherein such genetic modificationsresult in increased efficiency of butanol production. In somemodifications the clostridia species is Clostridium beijerinckii whichis an anaerobic bacterium known for the fermentative production ofacetone and butanol. In some embodiments, the genetic modifications areintroduced by genetic recombination. In some embodiments, the geneticmodifications are introduced by nucleic acid transformation.

Described herein are methods for producing genetically-modifiedsolventogenic organism strains wherein such genetic modifications resultin increased efficiency of solvent production. Described herein aremethods for identifying genetic signatures associated with increasedefficiency of butanol production wherein the genetic signatures include,but are not limited to, increased or decreased expression of genesrelated to butanol production pathway and variants thereof, and modifiedor altered sequences of genes involved in or related to the butanolproduction pathway. Genes and sequence variants thereof that have beenidentified in relation to increased efficiency of solvent production areused to transform bacteria (e.g., clostridia) or other microorganismsand increased or decreased expression of these genes are correlated withmore efficient butanol production by these recombinant solventogenicorganisms.

Increased efficiency of solvent production can be determined in anynumber of ways including but not limited to: concentration(weight/volume) of solvent in fermentation medium, yield (weight/weight)of solvent per amount of substrate, and rate of solvent formation(weight/volume/time).

Described herein are recombinant solventogenic organism strainscomprising increased expression of a gene selected from the groupconsisting of Adh, Bcd, and Buk and variants thereof, relative to theorganism strain prior to its transformation.

Described herein are recombinant solventogenic organisms comprisingincreased expression of a gene selected from the group consisting ofCheA, CheC, and CheD and variants thereof relative to the organismstrain prior to its transformation.

Described herein are recombinant solventogenic organisms comprisingdecreased expression of a gene selected from the group consisting ofManIIAB and ManIIC and variants thereof relative to the organism strainprior to its transformation.

Described herein are recombinant solventogenic organisms comprisingdecreased expression of a gene selected from the group consisting ofSpoIVA, SpoVB, and SspA and variants thereof relative to the organismstrain prior to its transformation.

In some variations, the recombinant solventogenic organisms describedherein comprise a heterologous nucleic acid sequence. In somevariations, the recombinant solventogenic organisms described hereincomprise an introduced heterologous nucleic acid. In some variations,expression of the heterologous nucleic acid sequence is controlled by aninducible promoter. In some variations, expression of the heterologousnucleic acid sequence is controlled by a constitutive promoter.

In some variations, the recombinant solventogenic organisms describedherein comprise an mRNA resulting from transcription of the heterologousnucleic acid sequence, wherein the mRNA accumulates to a higher or lowerlevel relative to the organism strain prior to transformation.

In some variations, the recombinant solventogenic organisms describedherein comprise a protein resulting from the heterologous nucleic acid,and the protein accumulates to a higher or lower level relative to theorganism strain prior to its transformation.

In some variations, the recombinant solventogenic organisms describedherein comprise a protein with an altered activation state which iscorrelated with increased production of a solvent, relative to theorganism strain prior to its transformation.

In some variations, the recombinant solventogenic organisms describedherein are yeast.

In some variations, the recombinant solventogenic organisms describedherein are bacteria. In some variations, the recombinant solventogenicorganisms described herein are Escherichia. In some variations, therecombinant solventogenic organisms described herein are Escherichiacoli. In some variations, the recombinant solventogenic organismsdescribed herein are Clostridium. In some variations, the recombinantsolventogenic organisms described herein are Clostridium beijerinckii.In some variations, the recombinant solventogenic organisms describedherein are Clostridium acetobutylicum.

In some variations, the recombinant solventogenic organisms describedherein are cellulolytic.

In some variations, the recombinant solventogenic organisms describedherein are non-cellulolytic.

In some variations, the recombinant solventogenic organisms describedherein comprise an siRNA, DNAzyme, or antisense nucleic acid.

In some variations, the recombinant solventogenic organisms describedherein comprise a heterologous nucleic acid from a Clostridium. In somevariations, the recombinant solventogenic organisms described hereincomprise a heterologous nucleic acid from a solventogenic Clostridium.In some variations, the recombinant solventogenic organisms describedherein a heterologous nucleic acid from a Clostridium beijerinckii. Insome variations, the recombinant solventogenic organisms describedherein comprise a heterologous nucleic acid from Clostridiumbeijerinckii 8052. In some variations, the recombinant solventogenicorganisms described herein comprise a heterologous nucleic acid fromClostridium beijerinckii BA101.

In some variations, the recombinant solventogenic organisms describedherein produce butanol. In some variations, the recombinantsolventogenic organisms described herein produce ethanol. In somevariations, the recombinant solventogenic organisms described hereinproduce acetone.

Described herein are methods of producing a solvent comprising culturingthe recombinant solventogenic organisms described herein.

Described herein are methods for producing butanol, comprising culturingthe recombinant solventogenic organisms described herein.

Described herein are methods for producing ethanol, comprising culturingthe recombinant solventogenic organisms described herein.

Described herein are methods of identifying a gene related to productionof a solvent comprising culturing cells in a medium comprising amaterial which can be acted on to produce the solvent, comprisingmeasuring the level of the solvent, and correlating an accumulation of aspecific mRNA population via microarray with production of the solvent.

Described herein are methods of identifying the solventogenic potentialof an organism comprising culturing cells in a medium comprising amaterial which can be acted on to produce the solvent, and correlatingan accumulation of an mRNA population selected from the group consistingof Adh, Bcd, Buk, CheA, CheC, CheD, ManIIAB, ManIIC, SpoIVA, SpoVB, andSspA mRNA. In some variations the organism is yeast. In some variationsthe organism is bacteria. In some variations the organism is anEscherichia coli. In some variations the organism is a Clostridium. Insome variations the organism is a Clostridium beijerinckii. In somevariations the organism is a Clostridium acetobutylicum. In somevariations the organism is cellulolytic. In some variations the organismis non-cellulolytic. In some variations the organism is recombinant.

These and other embodiments, features and advantages will become moreapparent to those skilled in the art when taken with reference to thefollowing more detailed description of the invention in conjunction withthe accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the Office upon request and paymentof the necessary fee.

The accompanying drawings, which are incorporated herein and constitutepart of this specification, illustrate presently preferred embodimentsof the invention, and, together with the general description given aboveand the detailed description given below, serve to explain features ofthe invention.

FIG. 1A and FIG. 1B depict growth curves (A) and pH profiles (B),respectively, for the fermentor cultures of C. beijerinckii NCIMB 8052(♦) and C. beijerinckii BA101 (o). This figure is described in Example2.

FIG. 2A, FIG. 2B and FIG. 2C depict formation of total solvents (A),butanol (B), and acetone (C), respectively, in the fermentor cultures ofC. beijerinckii NCIMB 8052 (♦) and C. beijerinckii BA101 (o). Timecourses are shown for the production of solvents in C. beijerinckiiBA101 in comparison with C. beijerinckii NCIMB 8052. This figure isdescribed in Example 2.

FIG. 3A and FIG. 3B depict mRNA accumulation profiles analyzed by DNAmicroarray for C. beijerinckii NCIMB 8052 and C. beijerinckii BA101,respectively, over the time course of fermentation. This figure is incolor, and is described in Example 4.

FIG. 4 quantitatively depicts differential mRNA accumulation ofsolventogenic genes in C. beijerinckii NCIMB 8052 (♦) and C.beijerinckii BA101 (o). Increased expression in C. beijerinckii BA101during the solventogenic stage is shown for alcohol dehydrogenase (Adh),butyryl-CoA dehydrogenase (Bcd) and butyrate kinase (Buk). This figureis described in Example 4.

FIG. 5 depicts differential mRNA accumulation of sugar transporters inC. beijerinckii NCIMB 8052 (♦) and C. beijerinckii BA101 (o). Componentsof mannose-family phosphoenolpyruvate (PEP)-dependent phosphotransferasesystem IIA, IIB (ManIIAB) and IIC (ManIIC) were significantlydown-regulated in C. beijerinckii BA101. This figure is described inExample 4.

FIG. 6 depicts differential mRNA accumulation of sporulation genes in C.beijerinckii NCIMB 8052 (♦) and C. beijerinckii BA101 (o). Induction oflate stage sporulation factors was much weaker in C. beijerinckii BA101than in the wild-type strain. Lowered activation in C. beijerinckiiBA101 through the solventogenic phase is shown for coat morphosissporulation protein (SpoIVA), Stage V sporulation protein B (SpoVB) andsmall acid-soluble spore protein (SspA). This figure is described inExample 4.

FIG. 7 depicts differential mRNA accumulation of chemotaxis genes in C.beijerinckii NCIMB 8052 (♦) and C. beijerinckii BA101 (o). Higherexpression levels of CheA, CheC, CheD and CheW in a chemotaxis genecluster are shown for C. beijerinckii BA101 during the solventogenicstage.

FIG. 8 depicts solventogenic mRNAs with comparable accumulation kineticsin C. beijerinckii NCIMB 8052 (♦) and C. beijerinckii BA101 (o).Expression of aceto-acetyl CoA:acetate-butyrate CoA transferase subunitα/β (CtfA/B) and acetoacetate decarboxylase (Adc) were highly activatedat the onset of solventogenic phase in C. beijerinckii BA101 and C.beijerinckii NCIMB 8052. Changes in expression levels were much smallerfor thiolase (Thl), 3-hydroxybutyryl-CoA dehydrogenase (Hcd) andcrotonase (Crt) in C. beijerinckii BA101 and C. beijerinckii NCIMB 8052.This figure is described in Example 4.

FIG. 9 depicts reactions in the clostridial solventogenic pathway. Genesinvolved in catalyzing the conversion of intermediate metabolites areindicated.

FIG. 10 shows the Adh (Alcohol dehydrogenase) gene Cbei_(—)2181 of C.beijerinckii NCIMB 8052 DNA sequence (SEQ ID NO: 1).

FIG. 11 shows the Bcd (Butyryl-CoA dehydrogenase) gene Cbei_(—)2035 ofC. beijerinckii NCIMB 8052 DNA sequence (SEQ ID NO: 2).

FIG. 12 shows the Buk (Butyrate kinase) C. beijerinckii NCIMB 8052 DNAsequence (SEQ ID NO: 3).

FIG. 13 shows the CheA (Chemotaxis protein) C. beijerinckii NCIMB 8052DNA sequence (SEQ ID NO: 4).

FIG. 14 shows the CheC (Chemotaxis protein) C. beijerinckii NCIMB 8052DNA sequence (SEQ ID NO: 5).

FIG. 15 shows the CheD (Chemotaxis protein) C. beijerinckii NCIMB 8052DNA sequence (SEQ ID NO: 6).

FIG. 16 shows the ManIIAB (Mannose-specific PTS system component IIAB)C. beijerinckii NCIMB 8052 DNA sequence (SEQ ID NO: 7).

FIG. 17 shows the ManIIC (Mannose-specific PTS system component IIC) C.beijerinckii NCIMB 8052 DNA sequence (SEQ ID NO: 8).

FIG. 18 shows the SpoIVA (Stage 1V sporulation protein A) C.beijerinckii NCIMB 8052 DNA sequence (SEQ ID NO: 9).

FIG. 19 shows the SpoVB (Stage V sporulation protein B) C. beijerinckiiNCIMB 8052 DNA sequence (SEQ ID NO: 10).

FIG. 20 shows the SspA (Small acid-soluble spore protein) C.beijerinckii NCIMB 8052 DNA sequence (SEQ ID NO: 11).

The DNA sequence (SEQ ID NO: 12) of the Cbei_(—)0322 gene homologous toBcd (Butyryl-CoA dehydrogenase) gene Cbei_(—)2035 of C. beijerinckiiNCIMB 8052 is shown in FIG. 21A and the protein sequence of Cbei_(—)0322(SEQ ID NO: 13) shown in FIG. 21B.

The DNA sequence (SEQ ID NO: 14) of the Cbei_(—)1722 gene homologous tothe Adh (Alcohol dehydrogenase) gene Cbei_(—)2181 of C. beijerinckiiNCIMB 8052 is shown in FIG. 22A and predicted amino acid sequence (SEQID NO: 15) of Cbei_(—)1722 is shown in FIG. 22B.

The DNA sequence of Cbei_(—)3111 (SEQ ID NO: 16) homologous to SspA(Small acid-soluble spore protein) gene Cbei_(—)3080 of C. beijerinckiiNCIMB 8052 is shown in FIG. 23A and the protein sequence of Cbei_(—)3111(SEQ ID NO: 17) shown in FIG. 23B.

The DNA sequence of Cbei_(—)3250 (SEQ ID NO: 18) homologous to SspA(Small acid-soluble spore protein) gene Cbei_(—)3080 of C. beijerinckiiNCIMB 8052 is shown in FIG. 24A and the protein sequence of Cbei_(—)3250(SEQ ID NO: 19) shown in FIG. 24B.

DETAILED DESCRIPTION OF THE INVENTION

The detailed description illustrates by way of example, not by way oflimitation, the principles of the invention. It is to be understood thatthis invention is not limited to the particular methodology, protocols,cell lines, constructs, and reagents described herein and as such mayvary. It is also to be understood that the terminology used herein isfor the purpose of describing particular embodiments only, and is notintended to limit the scope of the present invention, which will belimited only by the appended claims. Hence, the invention is not limitedto the preferred embodiments described exemplarily herein. Moreover,this description will clearly enable one skilled in the art to make anduse the invention, and describes several embodiments, adaptations,variations, alternatives and uses of the invention, including what ispresently believed by applicant to be the best mode of carrying out theinvention.

As used herein and in the appended claims, the singular forms “a,” “an,”and “the” include plural reference unless the context clearly indicatesotherwise. For example, reference to “alcohol dehydrogenase” is areference to one or more such proteins and includes variants andequivalents thereof known to those skilled in the art.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art to which this invention belongs. Although any methods, devices,and materials similar or equivalent to those described herein can beused in the practice or testing of the invention, the preferred methods,devices and materials are now described. The publications discussedherein are provided solely for their disclosure prior to the filing dateof the present application. Nothing herein is to be construed as anadmission that the inventors are not entitled to antedate suchdisclosure by virtue of prior invention or for any other reason.

This invention utilizes routine techniques in the field of recombinantgenetics. Basic texts disclosing the general methods of use in thisinvention include Sambrook et al., Molecular Cloning, A LaboratoryManual (3rd ed. 2001); Kriegler, Gene Transfer and Expression: ALaboratory Manual (1990); and Current Protocols in Molecular Biology(Ausubel et al., eds., 1994)). General texts which describe molecularbiological techniques include Berger and Kimmel, Guide to MolecularCloning Techniques, Methods in Enzymology volume 152 Academic Press,Inc., San Diego, Calif. (Berger); Sambrook et al., Molecular Cloning—ALaboratory Manual (2nd Ed.), Vol. 1-3, Cold Spring Harbor Laboratory,Cold Spring Harbor, N.Y., 1989 (“Sambrook”) and Current Protocols inMolecular Biology, F. M. Ausubel et al., eds., Current Protocols, ajoint venture between Greene Publishing Associates, Inc. and John Wiley& Sons, Inc., (supplemented through 1999) (“Ausubel”)).

Described herein are 1) organisms for use in the methods andcompositions described herein; 2) methods of identifying organisms foruse in the methods and compositions described herein, 3) methods ofmodifying organisms, 4) methods of preparing substrates, 5) methods ofprocessing cellulose to sugars, 6) methods of generating solvents fromsugars, and 7) methods of optimizing organisms for use in industrialapplications.

Described herein are methods for identifying genetic signatures(increased or decreased expression of gene(s) or, variant genesequences) associated with a mutated clostridia (C. beijernicki BA101)that exhibits butanol production with increased efficiency relative tothe wild type clostridia (C. beijernicki NCIMB 8052)). Methods formodifying clostridia or other organisms to acquire such geneticsignatures wherein acquisition of the genetic signatures results inincreased efficiency of ethanol production are described herein.

Organisms for Use in the Methods and Compositions Described Herein

In the broadest sense, any prokaryotic or eukaryotic organism capable ofadaptation for use in the methods and compositions described herein maybe used in the methods and compositions described herein.

In some variations, bacteria, fungi, yeast or other organisms which areinitially solventogenic are used in the methods and compositionsdescribed herein. As used herein, a solventogenic organism is anorganism that is at least partially capable of producing a solvent suchas butanol, ethanol, acetone, or isopropanol. Non-limiting examples ofsolventogenic microorganisms include Clostridium species, such as C.beijerinckii, C. beijerinckii 8052, C. beijerinckii BA101, C.acetobutylicum, C. pasteurianum, C. butyricum, C. sporogenes, C.felsenium, C. saccharobutylicum, C. saccharoperbutylacetonicum, C.tetanomorphum, C. aurantibutyricum, C. cadaveris, C. puniceum and C.thermosaccharolyticum (Durre, P., Formation of solvents in Clostridia in‘Handbook on Clostridia’, P. Durre (ed.), CRC Press-Taylor & FrancisGroup, Boca Raton, Fla., USA, 2005), as well as C. algidixylanolyticum(D M Broda, et. al., Clostridium algidixylanolyticum sp. nov., apsychrotolerant, xylan-degrading, spore-forming bacterium. Int J SystEvol Microbiol 50: 623-631, 2000), C. thermopapyrolyticum (B S Mendez,et. al., Clostridium thermopapyrolyticum sp. nov., a cellulolyticthermophile. Int J Syst Bacteriol 41 (2):281-283, 1991) and C.carboxydivorans (J S Liou, et. al., Clostridium carboxydivorans sp.nov., a solvent-producing clostridium isolated from an agriculturalsettling lagoon, and reclassification of the acetogen Clostridiumscatologenes strain SL1 as Clostridium drakei sp. nov. Int J Syst EvolMicrobiol 55: 2085-2091, 2005), and some non-Clostridium species such asAnaerobacter polyendosporus (V I Duda, et. al., A new anaerobicbacterium, forming up to five endospores per cell—Anaerobacterpolyendosporus gen. et sp. nov. Arch Microbiol 148(2):121-127, 1987; A VSiunov, et. al., Phylogenetic status of Anaerobacter polyendosporus, ananaerobic, polysporogenic bacterium. Int J Syst Bacteriol 49: 1119-1124,1999), Butyribacterium methylotrophicum (J G Zeikus, et. al., Isolationand characterization of a new, methylotrophic, acidogenic anaerobe, theMarburg strain. Curr Microbiol 3(6):381-386, 1980; G-J Shen, et. al.,Biochemical basis for carbon monoxide tolerance and butanol productionby Butyribacterium methylotrophicum. Appl Microbiol Biotechnol 51:827-832, 1999), Thermoanaerobacterium thermosaccharolyticum andThermoanaerobacterium strain Mel9 (M D Collins, et. al., The phylogenyof the genus Clostridium: proposal of five new genera and eleven newspecies combinations. Int J Syst Bacteriol 44: 812-826, 1994; P GStroot, et. al., Description of a new butanol-producing thermophileThermoanaerobacterium strain Mel9. In Abstracts of the 99th Meeting ofthe American Society for Microbiology, 1999), and Thermohydrogeniumkirishiense (E V Zacharova, et. al., Thermohydrogenium kirishiense gen.nov. and sp. nov., a new anaerobic thermophilic bacterium. ArchMicrobiol 160: 492-497, 1993).

Anaerobic spore-forming bacteria belonging to the genus Clostridium havebeen useful in industrial applications including enzyme and solventproduction. Among saccharolytic butyric acid-producing clostridia, thereare a number of species capable of producing significant amounts ofneutral solvents during the later stages of a batch fermentation underappropriate conditions. The strain used most extensively for theproduction of acetone and butanol are generally classified as C.acetobutylicum. A number of different species of butanol-producingclostridia are recognized based on differences in the type and ratio ofthe solvents produced. C. beijerinckii (C. butylicum) produces solventsin approximately the same ratio as C. acetobutylicum, howeverisopropanol is produced in place of acetone. C. aurantibutyricumproduces both acetone and isopropanol in addition to butanol. C.tetanomorphum produces almost equimolar amounts of butanol and ethanolbut no other solvents. (Jones and Woods (1986) supra).

Advantages of using C. beijerinckii over C. acetobutylicum includebroader substrate range and better pH range, ability to produce butanolduring log-phase growth, stability with respect to strain degeneration,and ability to use a variety of substrates to produce butanol. Moreover,the solventogenic genes on C. beijerinckii are located on thechromosome, whereas the genes are located on a plasmid in C.acetobutylicum. Thus C. beijerinckii is more genetically stable.

In some variations, bacteria, fungi, yeast or other organisms which arenot initially solventogenic are used in the methods and compositionsdescribed herein.

Non-limiting examples of the organisms described herein includeClostridium sp. In some variations the Clostridium is C.phytofermentans, C. thermohydrosulfuricum, C. absonum, C. absonum, C.acidisoli, C. akagii, C. algidixylanolyticum, C. bowmanii, C.cellulolyticum, C. cylindrosporum, C. diolis, C. estertheticum, C.estertheticum, C. estertheticum, C. frigidicarnis, C. frigidicarnis, C.frigoris, C. glycolicum, C. papyrosolvens, C. perfringens, C.pseudotetanicum, C., C. psychrophilum, C. rubrum, C. sardiniense, C.sardiniense, C. thermocellum, C. celerecrescens, C. lentocellum, C.polysaccharolyticum, C. populeti, C. thermohydrosulfuricum, C.thermocellum, C. cellulovorans, or C. josui.

In some variations, the organisms described herein include Escherichiasp., including E. coli, Saccharomyces sp., including S. cerevisiae, andvarious Cyanobacteria.

In some variations, the organisms described herein include Aspergillussp., Bacillus sp., Brevibacterium sp., Clostridium sp., Corynebacteriumsp., Gluconobacter sp., Pseudomonas sp., Rhodococcus sp., Streptomycessp., Xanthomonas sp., Candida sp., and Zymomonas sp.

In some variations the organisms described herein includeAcidithiobacillus sp., Acinetobacter sp., Allochromatium sp.,Azotobacter sp., Bacillus sp., Bdellovibrio sp., Cellulomonas sp.,Desulfovibrio sp., Geobacillus sp., Gluconobacter sp., Kocuria sp.,Lactobacillus sp., Leuconostoc sp., Myxococcus sp., Pediococcus sp.,Propionibacterium sp., Pseudomonas sp., Raoultella sp., Rhizobium sp.,Rhodospirillum sp., Sporosarcina sp., Streptomyces sp., Thermus sp.,Thiobacillus sp., Variovorax sp., Vibrio sp., Wautersia sp., andZymomonas sp.

In some variations the organisms described herein include Selenomonassp., Methanobrevibacter sp., Ruminococcus sp., Fibrobacter sp.,Prevotella sp., Treponema sp., Azospirillum sp., Cellulomonas sp., andTrichoderma sp.

In some variations the organisms described herein include Acremoniumsp., Alternaria sp., Aureobasidium sp., Botrytis sp., Chaetomium sp.,Dipodascus sp., Endomyces sp., Eremascus sp., Geotrichum sp., Humicolasp., Neurospora sp., Penicillium sp., Pichia sp., Schizosaccharomycessp., Sordaria sp., and Sordaria sp.

In some variations the organisms described herein are cellulolytic. Insome variations the organisms described herein are non-cellulolytic.

Methods of Identifying Organisms

Described herein are methods of identifying organisms for use in themethods and compositions described herein. Unless the context clearlyindicates otherwise, any organism described herein may be identified bythe methods described herein.

In some variations, organisms are screened for their ability to producea particular product or products from one or more starting materials. Insome variations, a culture medium or organisms in a culture medium arescreened for the presence, absence, or level of a particular product. Insome variations, a culture medium or organisms in a culture medium arescreened for the presence, absence or level of a particular solvent,including but not limited to butanol, ethanol, or acetone. By way ofnonlimiting example, screening for products or solvents may be via HPLC,mass spectrometry, GC, immunoassay, activity assay, or other methodsknown by those of skill in the art.

In some variations, an organism is screened for the presence, absence,or amount of a particular gene or gene product.

In some variations, DNA is screened for the presence, or absence, orcopy number of a particular gene. By way of nonlimiting example,screening of DNA may be via Southern blot hybridization, PCR,microarray, or other methods known by those of skill in the art. In somevariations genomic or non-genomic DNA is screened via microarray for thepresence or absence of a particular gene.

In some variations, an organism's mRNA is screened for the presence,absence, or amount of a particular mRNA species. By way of nonlimitingexample, screening of mRNA may be via Northern blot hybridization, PCR,microarray, or other methods known by those of skill in the art. In somevariations, an organism's mRNA is screened via microarray for thepresence, absence, or amount of a particular mRNA. In some variations,an organism's mRNA is screened via the method described in Example 4 forthe presence, absence or amount of a particular mRNA species.

In some variations, an organism's mRNA is screened for the presence of aparticular mRNA species.

In some variations, an organism's mRNA is screened for an amount of aparticular mRNA species. In some variations, a recombinant organism'smRNA is screened for an amount of a particular mRNA species, relative tothe organism strain prior to its transformation.

In some variations, a recombinant organism is screened for a decreasedlevel of a particular mRNA species, relative to the organism strainprior to its transformation. In some variations, a recombinant organismis screened for an amount of decrease in level of a particular mRNAspecies, relative to the organism strain prior to its transformation,wherein the decreased mRNA species is used by a pathway that limits theability of the recombinant organism to produce a preferred solvent. Insome variations the amount of decrease of the mRNA species is 5%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,90%, 95%, 100%, relative to the organism strain prior to itstransformation.

In some variations, an organism's mRNA is screened for an increasedlevel of a particular mRNA species. In some variations, a recombinantorganism's mRNA is screened for an increased level of a particular mRNAspecies, relative to the organism strain prior to its transformation. Insome variations, a recombinant organism's mRNA is screened for anincreased level of a particular mRNA species relative to the organismstrain prior to its transformation, wherein the level of the particularmRNA species is increased at least 1.5-fold, 2-fold, 4-fold, 10-fold,25-fold, 50-fold, 100-fold relative to the organism strain prior to itstransformation. In some variations, a recombinant organism's mRNA isscreened for an increased level of a particular mRNA species relative tothe organism strain prior to its transformation, wherein the level ofthe particular mRNA species is increased at least 2-fold. In somevariations, a recombinant organism's mRNA is screened for an increasedlevel of a particular mRNA species relative to the organism strain priorto its transformation, wherein the level of the particular mRNA speciesis increased at least 5-fold. In some variations, a recombinantorganism's mRNA is screened for an increased level of a particular mRNAspecies relative to the organism strain prior to its transformation,wherein the level of the particular mRNA species is increased at least10-fold. In some variations, a recombinant organism's mRNA is screenedfor an increased level of a particular mRNA species relative to theorganism strain prior to its transformation, wherein the level of theparticular mRNA species is increased at least 15-fold. In somevariations, a recombinant organism's mRNA is screened for an increasedlevel of a particular mRNA species relative to the organism strain priorto its transformation, wherein the level of the particular mRNA speciesis increased at least 20-fold.

In some variations, an organism's proteins are screened for thepresence, absence, or amount of a particular protein, or activationstate of a particular protein. By way of nonlimiting example, screeningof proteins may be via Western blot hybridization, immunoassay, activityassay, microarray, various fluorescence and flow cytometry methodsincluding fluorescence-activated cell sorting, or other methods known bythose of skill in the art.

In some variations, an organism's proteins are screened for an amount ofa particular protein species. In some variations, a recombinantorganism's proteins are screened for an amount of a particular proteinspecies, relative to the organism strain prior to its transformation.

In some variations, a recombinant organism is screened for a decreasedlevel of a particular protein species, relative to the organism strainprior to its transformation. In some variations, a recombinant organismis screened for a decrease in amount of a particular protein species,relative to the organism strain prior to its transformation, wherein thedecreased protein species is used by a pathway that limits the abilityof the recombinant organism to produce a preferred solvent. In somevariations the amount of decrease of the protein species is 5%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,90%, 95%, 100%, relative to the organism strain prior to itstransformation.

In some variations, an organism's proteins are screened for an increasedlevel of a particular protein species. In some variations, a recombinantorganism strain's proteins are screened for an increased level of aparticular protein species, relative to the organism strain prior to itstransformation. In some variations, a recombinant organism's proteinsare screened for an increased level of a particular protein speciesrelative to the organism strain prior to its transformation, wherein thelevel of the particular protein species is increased about 1.5-fold,2-fold, 5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold,80-fold, or 100-fold relative to the organism strain prior to itstransformation. In some variations, a recombinant organism's proteinsare screened for an increased level of a particular protein speciesrelative to the organism strain prior to its transformation, wherein thelevel of the particular protein species is increased at least 2-fold. Insome variations, a recombinant organism's proteins are screened for anincreased level of a particular protein species relative to the organismstrain prior to its transformation, wherein the level of the particularprotein species is increased at least 5-fold. In some variations, arecombinant organism's proteins are screened for an increased level of aparticular protein species relative to the organism strain prior to itstransformation, wherein the level of the particular protein species isincreased at least 10-fold. In some variations, a recombinant organism'sproteins are screened for an increased level of a particular proteinspecies relative to the organism strain prior to its transformation,wherein the level of the particular protein species is increased atleast 20-fold. In some variations, a recombinant organism's proteins arescreened for an increased level of a particular protein species relativeto the organism strain prior to its transformation, wherein the level ofthe particular protein species is increased up to about 80-fold.

In some variations, an organism's proteins are screened for a level of aparticular activated protein species. In some variations a protein isactivated by phosphorylation, dephosphorylation, cleavage, refolding, orassociation with another molecule, including but not limited to anotherprotein.

In some variations, an organism's proteins are screened for a level of aparticular activated protein species. In some variations, a recombinantorganism's proteins are screened for a level of a particular activatedprotein species, relative to the organism strain prior to itstransformation.

In some variations, a recombinant organism is screened for a decreasedlevel of a particular activated protein species, relative to theorganism strain prior to its transformation. In some variations, arecombinant organism is screened for a decrease in level of a particularactivated protein species, relative to the organism strain prior to itstransformation, wherein the decreased activated protein species is usedby a pathway that limits the ability of the recombinant organism toproduce a preferred solvent. In some variations the amount of decreaseof the activated protein species is 5%, 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 100%, relative tothe organism strain prior to its transformation.

In some variations, a recombinant organism's proteins are screened foran increased level of a particular activated protein species, relativeto the organism strain prior to its transformation. In some variations,a recombinant organism's proteins are screened for an increased level ofa particular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 1.5-fold, 2-fold,5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 80-fold,or 100-fold relative to the organism strain prior to its transformation.In some variations, a recombinant organism's proteins are screened foran increased level of a particular activated protein species relative tothe organism strain prior to its transformation, wherein the level ofthe particular activated protein species is increased at least 1.5-fold.In some variations, a recombinant organism's proteins are screened foran increased level of a particular activated protein species relative tothe organism strain prior to its transformation, wherein the level ofthe particular activated protein species is increased at least 5-fold.In some variations, a recombinant organism's proteins are screened foran increased level of a particular activated protein species relative tothe organism strain prior to its transformation, wherein the level ofthe particular activated protein species is increased at least 15-fold.In some variations, a recombinant organism's proteins are screened foran increased level of a particular activated protein species relative tothe organism strain prior to its transformation, wherein the level ofthe particular activated protein species is increased at least 20-fold.In some variations, a recombinant organism's proteins are screened foran increased level of a particular activated protein species relative tothe organism strain prior to its transformation, wherein the level ofthe particular activated protein species is increased up to about80-fold.

In some variations, an organism is screened for a level of a particularsolvent. In some variations, a recombinant organism is screened for alevel of a particular solvent, relative to the organism strain prior toits transformation.

In some variations, a recombinant organism is screened for a decreasedlevel of a particular solvent, relative to the organism strain prior toits transformation. In some variations, a recombinant organism isscreened for a decrease in level of a particular solvent, relative tothe organism strain prior to its transformation, wherein the decreasedsolvent is generated by a pathway that limits the ability of therecombinant organism to produce a preferred solvent. In some variations,the solvent which has been decreased is ethanol. In some variations, thesolvent which has been decreased is acetone. In some variations, thesolvent which has been decreased is butanol. In some variations theamount of decrease is 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 100%, relative to the organismstrain prior to its transformation.

Increased efficiency of solvent production can be determined in anynumber of ways including but not limited to: concentration(weight/volume) of solvent in fermentation medium, yield (weight/weight)of solvent per amount of substrate, and rate of solvent formation(weight/volume/time).

In one aspect of the invention, a recombinant organism strain isscreened for an increased level of a particular solvent, relative to theorganism strain prior to its transformation.

In some variations, recombinant solventogenic organism strains arescreened for producing an increased amount of a particular solventrelative to the organism strain prior to its transformation, wherein theamount of the particular solvent is increased at least 1.1, 1.2, 1.3,1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4,3.6, 3.8, 4.0, 4.5, 5.0, 5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5,10, 15, 20, 40, 60, 80, or 100-fold over that in the organism strainprior to its transformation.

Where the concentration of the solvent in the organism strain prior toits transformation is 10 g/L, the recombinant solventogenic organismstrains are screened for having concentrations of the solvent of about11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36,38, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 g/L.

In some variations, recombinant solventogenic organism strains arescreened for producing an increased yield of a particular solvent peramount of the substrate, relative to the organism strain prior to itstransformation. Where the yield of solvent in the organism strain priorto its transformation is about 20 g/g of substrate, recombinantsolventogenic organism strains of the present invention are screened forproducing yields of: 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 50,52, 56, 60, 64, 68, 72, 76, or 80 g solvent per g substrate.

In some variations, recombinant organism strains are screened fordisplaying an increased rate of formation of a particular solvent,relative to the organism strain prior to its transformation. Where therate of formation of solvent in the organism strain prior to itstransformation is about 0.2 g/L/hour of substrate recombinantsolventogenic organism strains are screened for producing rates ofsolvent formation of: 0.24, 0.26, 0.28, 0.3, 0.32, 0.34, 0.36, 0.38,0.4, 0.44, 0.48, 0.52, 0.56, 0.6, 0.64, 0.68, 0.72, 0.76, 0.8, 0.9, 1,1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 3, 4, 8, or 12 g/L/hr.

In some variations, a recombinant organism is screened for an increasedlevel of a particular solvent relative to the organism strain prior toits transformation, wherein the level of the particular solvent isincreased at least 0.05%, 0.1%, 0.15%, 0.2%, 0.25%, 0.3%, 0.35%, 0.4%,0.45%, 0.5%, 0.55%, 0.6%, 0.65%, 0.7%, 0.75%, 0.8%, 0.9%, 0.95%, 1%,1.1%, 1.2%, 1.3%, 1.4%, 1.5%, 1.6%, 1.7%, 1.8%, 1.9%, 2%, 2.1%, 2.2%,2.3%, 2.4%, 2.5%, 2.75%, 3%, 3.25%, 3.5%, 3.75%, 4%, 4.25%, 4.5%, or 5%.In some variations, a recombinant organism is screened for an increasedlevel of a particular solvent relative to the organism strain prior toits transformation, wherein the level of the particular solvent isincreased at least 5%, 0.10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 100%, 125%, 150%, 175%, 200%,225%, 250%, 275%, 300%., 325%, 350%, 375%, 400%, 425%, 450%, 475%, 500%,600%, 700%, 800%, 900%, or 1000%. In some variations, a recombinantorganism is screened for an increased level of a particular solventrelative to the organism strain prior to its transformation, wherein thelevel of the particular solvent is increased at least 25%. In somevariations, a recombinant organism is screened for an increased level ofa particular solvent relative to the organism strain prior to itstransformation, wherein the level of the particular solvent is increasedat least 50%. In some variations, a recombinant organism is screened foran increased level of a particular solvent relative to the organismstrain prior to its transformation, wherein the level of the particularsolvent is increased at least 75%. In some variations, a recombinantorganism is screened for an increased level of a particular solventrelative to the organism strain prior to its transformation, wherein thelevel of the particular solvent is increased at least 100%. In somevariations, a recombinant organism is screened for an increased level ofa particular solvent relative to the organism strain prior to itstransformation, wherein the level of the particular solvent is increasedat least 200%. In some variations, a recombinant organism is screenedfor an increased level of a particular solvent relative to the organismstrain prior to its transformation, wherein the level of the particularsolvent is increased between 0.05-500%. In some variations, arecombinant organism is screened for an increased level of a particularsolvent relative to the organism strain prior to its transformation,wherein the level of the particular solvent is increased between0.05-300%. In some variations, a recombinant organism is screened for anincreased level of a particular solvent relative to the organism strainprior to its transformation, wherein the level of the particular solventis increased between 0.5-500%. In some variations, a recombinantorganism is screened for an increased level of a particular solventrelative to the organism strain prior to its transformation, wherein thelevel of the particular solvent is increased between 5-500%. In somevariations, a recombinant organism is screened for an increased level ofa particular solvent relative to the organism strain prior to itstransformation, wherein the level of the particular solvent is increasedbetween 100-500%. In some variations, a recombinant organism is screenedfor an increased level of a particular solvent relative to the organismstrain prior to its transformation, wherein the level of the particularsolvent is increased between 10-100%. In some variations, a recombinantorganism is screened for an increased level of a particular solventrelative to the organism strain prior to its transformation, wherein thelevel of the particular solvent is increased between 500-1000%. In somevariations, the solvent is butanol.

In some variations the solventogenic potential of an organism isevaluated by screening for the presence, absence, or amount of aparticular DNA sequence, mRNA sequence, protein, reaction product orsolvent. By way of nonlimiting example, the presence, absence, or amountof a particular DNA sequence, mRNA sequence, protein, reaction productor solvent related to reactions or reaction pathways used in thegeneration of solvents may be evaluated. By way of nonlimiting example,the presence, absence, or amount of a particular DNA sequence, mRNAsequence, protein, reaction product or solvent related to reactions orreaction pathways used in the tolerance to solvents may be evaluated. Insome variations, the presence, absence, or amount of a particular DNAsequence, mRNA sequence, protein, reaction product or solvent related tosugar transporters relevant to the production of solvents is evaluated.In some variations, the presence, absence, or amount of a particular DNAsequence, mRNA sequence, protein, reaction product or solvent related tosporulation activities may be evaluated. In some variations, thepresence, absence, or amount of a particular DNA sequence, mRNAsequence, protein, reaction product or solvent related to chemotaxis maybe evaluated.

In some variations the solventogenic potential of an organism isevaluated by screening for the presence, absence, or amount of acombination of particular DNA sequences, mRNA sequences, proteins,products or solvents.

In some variations, the solventogenic potential of an organism isevaluated by transiently or stably transforming the organism with one ormore genes related to production of a solvent, and screening for aparticular product or solvent. In some variations, the solventogenicpotential of an organism is evaluated by transiently or stablytransforming the organism with one or more of the genes describedherein, including but not limited to the genes described in the methodsof processing cellulose to sugars, methods of generating solvents fromsugars, and methods of optimizing organisms for use in industrialapplications sections.

Methods of Modifying Organisms

In some variations, the organisms for use in the compositions andmethods described herein are modified in order to improve their abilityto produce a solvent, including but not limited to butanol, ethanol, oracetone. In some variations, the organisms for use in the compositionsand methods described herein are genetically-modified in order toimprove their ability to produce a solvent. In some variations, geneticmaterial is introduced into the organisms for use in the compositionsand methods described herein in order to improve their ability toproduce a solvent.

Described herein are recombinant solventogenic organisms. In somevariations the recombinant solventogenic organisms described herein haveincreased or decreased expression of a gene product relative to theorganism strain prior to its transformation. An “organism strain priorto its transformation,” as used herein refers to the starting organismstrain that was transformed, which transformation yielded therecombinant organism.

For the purposes of this invention, the term “transformation” is usedbroadly encompass all methods for introducing a particular nucleic acidsequence into an organism. Thus, the term “transformation” indicates thegenetic alteration of a cell resulting from the uptake and expression offoreign genetic material (DNA). Methods for uptake of foreign DNAinclude transduction, a process in which bacterial DNA is moved from onebacterium to another by a bacteriophage and bacterial conjugationwherein a living bacterial cell transfers genetic material throughcell-to-cell contact.

The term “transformation” also indicates the genetic alteration of acell resulting from the uptake and expression of a specific geneticsequence (altered or heterologous nucleic acid sequence) without uptakeof a foreign genetic material. The latter would include, but is notlimited to, sequence alterations induced by site-directed mutagenesis orgenetic recombination.

Information about site-directed mutagenesis is found in the followingpublications and references cited within: Ling et al., Approaches to DNAmutagenesis: an overview, Anal Biochem. 254(2): 157-178 (1997); Dale etal., Oligonucleotide-directed random mutagenesis using thephosphorothioate method, Methods Mol. Biol. 57: 369-374 (1996); Smith,In vitro mutagenesis, Ann. Rev. Genet. 19: 423-462 (1985); Botstein &Shortle, Strategies and applications of in vitro mutagenesis, Science229: 1193-1201 (1985); Kunkel et al., Rapid and efficient site-specificmutagenesis without phenotypic selection, Methods in Enzymol. 154,367-382 (1987); Zoller & Smith, Oligonucleotide-directed mutagenesis: asimple method using two oligonucleotide primers and a single-strandedDNA template, Methods in Enzymol. 154: 329-350 (1987).

A solventogenic organism, as used herein, is an organism capable ofproducing one or more solvents, including but not limited to butanol,ethanol, isopropanol or acetone.

A “recombinant organism,” as used herein, is a non-naturally occurringorganism with an introduced nucleic acid sequence. The introducednucleic acid sequence may be integrated into the organism's chromosome,or separate from the organism's chromosome. As nonlimiting examples, theintroduced nucleic acid may be a plasmid, a vector, a virus, a viralparticle, a bacteriophage, an artificial chromosome, a mini-chromosome,or a linear strand of single stranded or double stranded nucleic acid. Anucleic acid sequence may also be introduced by site directedmutagenesis or genetic recombination.

In some variations the introduced nucleic acid is a heterologous nucleicacid. A “heterologous nucleic acid,” as used herein, refers to asequence of nucleic acids derived from an organism strain different fromthe organism strain into which the nucleic acid is introduced.

There are many known methods of transiently or stably introducingnucleic acid into organisms. There are well-established strategies fornucleic acid transformation of bacteria in the literature, includingthose described in Mercenier and Chassy, Strategies for the developmentof bacterial transformation systems, Biochimie 70, 503-517 (1988),Trevors et al., Electrotransformation of Bacteria by Plasmid DNA, inGuide to Electroporation and Electrofusion, Ed. Chang, Chassy, Saundersand Sowers, Academic Press (1992), and Dower et al., Protocols for theTransformation of Bacteria by Electroporation, Ed. Chang, Chassy,Saunders and Sowers, Academic Press (1992), each of which isincorporated herein by reference in its entirety for all purposes.

There are well-established transformation systems for Clostridium sp. inthe literature, including Blaschek and White, Genetic systemsdevelopment in the clostridia, FEMS Microbiology Reviews 17, 349-356(1995); Chen et al., Factors involved in the transformation ofpreviously non-transformable Clostridium perfringens type B., FEMSMicrobiol Lett. 140(2-3):185-91 (1996); Phillips-Jones, Introduction ofRecombinant DNA into Clostridium spp., in Electroporation Protocols forMicroorganisms, Ed. Jac Nickoloff, Humana Press (1995); Young et al.,Genetic Methods in Clostridia, in Methods in Microbiology, Vol. 29, Ed.Margaret Smith and R. Elizabeth Sockett, Academic Press (1999); andRood, Genetic Analysis in Clostridium perfringens, in The Clostridia:Molecular Biology and Pathogenesis, Ed. Rood, McClane, Songer andTitball, Academic Press (1997), each of which is incorporated herein byreference in its entirety for all purposes.

Nucleic acid molecules may be introduced into the yeast cells bystandard yeast transformation methods such as Lithiumacetate/single-stranded carrier DNA/polyethylene glycol method; FrozenYeast Protocol using frozen yeast cells that are competent fortransformation after thawing; Gene Gun Transformation using gold ortungsten nanoparticles coated with DNA that can be shot into cells; andProtoplast Transformation. See e.g., Sambrook et al., Molecular Cloning:A Laboratory Manual, 3d Ed., Cold Spring Harbor Press, Plainsview, N.Y.(2000). The transforming DNA may or may not be integrated into thegenome of the yeast cell. Upon the co-transformation of a linearizedvector and a nucleic acid molecule into a yeast cell, the nucleic acidmolecule is inserted into the insertion site via gap repair, anendogenous homologous recombination system in S. cerevisiae.

By way of nonlimiting example, to construct a solvent-producingclostridia, including but not limited to a C. beijerinckii, C.beijerinckii NCIMB 8052, or C. beijerinckii BA101 strain, one or moregenes related to solvent production may be expressed or overexpressed.Such genes may be isolated from another organism, including but notlimited to different clostridia or butanol-producing clostridia. Thoseof skill in the art are familiar with the tools for genetic manipulationof clostridia, including but not limited to appropriate source DNA,promoters, enhancers, terminators, integration vectors, autonomouslyreplicating vectors, transformation systems, enhanced- or site-specificrecombination systems, transposons, mobile intron systems and culturemedia.

In some variations, an organism described herein is transformed with oneor more genes expressible in the organism.

In some variations, an organism described herein is transformed with agene from a cellulolytic organism. In some variations, an organismdescribed herein is transformed with a gene from a non-cellulolyticorganism.

In some variations, an organism described herein is transformed with agene from a Clostridium strain. In some variations, an organismdescribed herein is transformed with a gene from Clostridiumbeijerinckii.

In some variations, an organism described herein is transformed with oneor more genes which have been altered so as to be better expressed inthe organism. In some variations, an organism described herein istransformed with one or more genes which have been codon optimized foruse in the organism. In some variations, an organism described herein istransformed with one or more genes which have been altered viasite-directed mutagenesis to improve production of a particular solventin the organism.

In some variations, an organism described herein is modified by randommutagenesis to improve production of a particular solvent in theorganism.

In some variations, an organism described herein is transformed with oneor more genes under the control of an inducible promoter. In somevariations, an organism described herein is transformed with one or moregenes under the control of a constitutive promoter.

In some variations, one or more of genes of interest is amplified viaPCR from a solventogenic organism such as a clostridium or, morespecifically, C. beijerinckii or C. beijerinckii BA101. In somevariations a promoter active in clostridia is used. In some variations aterminator active in clostridia is used. In some variations anintegration vector which allows insertion of genes into clostridia isused. In some variations a self-replicating or suicide vector whichallows expression of heterologous genes in clostridia is used. (FlaviaRamirez; M S Thesis; University of Illinois—Urbana Champaign). In somevariations, potential transformants bearing the target gene will beidentified via one or more selectable or detectable markers. In somevariations, potential transformants are analyzed by Southern blothybridization, PCR, and/or activity assay. The engineered Clostridiastrain may further be evaluated for solvent production, including butnot limited to butanol, ethanol or acetone production.

In some variations, a yeast strain is used in a process to produce oneor more solvents. Described herein are yeast strains wherein metabolicengineering and/or functional genomics have been utilized to optimizethe yeast strain's solventogenic potential. Compared to a nativebutanol-producing host, such as Clostridia, the yeast Saccharomycescerevisiae has several advantages. For example, S. cerevisiae is robust,displays a different tolerance to concentrations of product andinhibitors present in lignocellulosic hydrolysates, and is viable at asomewhat different pH range. In addition, yeast has a short doublingtime, its genetics and physiology is well-studied, and many geneticengineering tools are available.

There are well-established strategies for transformation of yeast in theliterature, including those described in Becker and Guarente, Protocolfor High-Efficiency Yeast Transformation, in Guide to Electroporationand Electrofusion, Ed. Chang, Chassy, Saunders and Sowers, AcademicPress (1992), which is incorporated herein by reference in its entiretyfor all purposes.

By way of nonlimiting example, to construct a solvent-producing yeast,including but not limited to a S. cerevisiae strain, one or more genesrelated to solvent production may be expressed or overexpressed. Suchgenes may be isolated from another organism, including but not limitedto the native butanol producer clostridia. Those of skill in the art arefamiliar with the tools for genetic manipulation of yeast, including butnot limited to appropriate source DNA, promoters, enhancers,terminators, integration vectors, transformation systems, and culturemedia.

The present invention relates to methods of obtaining the disclosednucleic acid molecules and proteins and of using the disclosed nucleicacid molecules, proteins, fragments of proteins for gene identificationand analysis, preparation of constructs, transformation of cells.

The term “an isolated nucleic acid” refers to a nucleic acid that is nolonger accompanied by some of materials with which it is associated inits natural state or to a nucleic acid the structure of which is notidentical to that of any of naturally occurring nucleic acid. Examplesof an isolated nucleic acid include: DNA which has the sequence of partof a naturally occurring genomic DNA molecules, but are not flanked bytwo coding sequences that flank that part of the molecule in the genomeof the organism in which it naturally occurs; a nucleic acidincorporated into a vector or into the genomic DNA of a prokaryote oreukaryote in a manner such that the resulting molecule is not identicalto any naturally occurring vector or genomic DNA; a separate moleculesuch as a DNA, a genomic fragment, a fragment produced by polymerasechain reaction (PCR), or a restriction fragment; recombinant DNAs; andsynthetic DNAs. An isolated nucleic acid may also be comprised of one ormore segments of DNA, genomic DNA or synthetic DNA.

In some variations, one or more of genes of interest is amplified viaPCR from a solventogenic organism such as a clostridium or, morespecifically, C. beijerinckii or C. beijerinckii BA101. In somevariations a promoter active in yeast, such as PyK or PGK, is used. Insome variations a terminator active in yeast, such as CYC1 terminator,is used. In some variations a yeast delta integration vector whichallows sequential insertion of multiple cloned genes into the yeastdispersed chromosomal sites is used. In some variations, potentialtransformants bearing the target gene will be identified via one or moreselectable or detectable markers. In some variations, potentialtransformants are analyzed by Southern blot hybridization, PCR, and/oractivity assay. The engineered yeast or S. cerevisiae strain may furtherbe evaluated for solvent production, including but not limited tobutanol, ethanol or acetone production. In some variations theengineered yeast or S. cerevisiae strain is evaluated for butanolproduction.

In some variations, an organism described herein is optimized todecrease production of one or more gene products which compete with orare otherwise detrimental to the production of solvents. In somevariations an organism described herein is transformed with a nucleicacid to decrease or impair expression of one or more gene products whichcompete with or are otherwise detrimental to the production of solvents.

In some variations, siRNA, DNAzymes, antisense, promoter inactivation,repressors, or other methods known by those of skill in the art are usedto decrease production of one or more gene products which compete withor are otherwise detrimental to the production of solvents.

In some variations, a recombinant organism described herein has analtered level of a particular solvent. In some variations, a recombinantorganism has an altered level of a particular solvent, relative to theorganism strain prior to its transformation.

In some variations, a recombinant organism comprises a decreased levelof a particular solvent, relative to the organism strain prior to itstransformation. In some variations, a recombinant organism comprises adecrease in level of a particular solvent, relative to the organismstrain prior to its transformation, wherein the decrease in level of theparticular solvent is used by a pathway that limits the ability of therecombinant organism to produce a preferred solvent. In some variations,the solvent which has been decreased is ethanol. In some variations, thesolvent which has been decreased is acetone. In some variations, thesolvent which has been decreased is butanol. In some variations theamount of decrease is 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%,55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 100%, relative to the organismstrain prior to its transformation.

In some variations, an organism comprises an altered level of aparticular mRNA species. In some variations, a recombinant organismcomprises an altered level of a particular mRNA species, relative to theorganism strain prior to its transformation.

In some variations, a recombinant organism comprises a decreased levelof a particular mRNA species, relative to the organism strain prior toits transformation. In some variations, a recombinant organism comprisesa decrease in level of a particular mRNA species, relative to theorganism strain prior to its transformation, wherein the decreased mRNAspecies is used by a pathway that limits the ability of the recombinantorganism to produce a preferred solvent. In some variations the amountof decrease of the mRNA species is 5%, 10%, 15%, 20%, 25%, 30%, 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 100%, relative tothe organism strain prior to its transformation.

In some variations, an organism comprises an altered amount of aparticular protein species. In some variations, a recombinant organismcomprises an altered amount of a particular protein species, relative tothe organism strain prior to its transformation.

In some variations, a recombinant organism comprises a decreased levelof a particular protein species, relative to the organism strain priorto its transformation. In some variations, a recombinant organismcomprises a decrease in level of a particular protein species, relativeto the organism strain prior to its transformation, wherein thedecreased protein species is used by a pathway that limits the abilityof the recombinant organism to produce a preferred solvent. In somevariations the amount of decrease of the protein species is 5%, 10%,15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%,90%, 95%, 100%, relative to the organism strain prior to itstransformation.

In some variations, an organism comprises an altered level of aparticular activated protein species. In some variations, a recombinantorganism comprises an altered level of a particular activated proteinspecies, relative to the organism strain prior to its transformation.

In some variations, a recombinant organism comprises a decreased levelof a particular activated protein species, relative to the organismstrain prior to its transformation. In some variations, a recombinantorganism comprises a decrease in level of a particular activated proteinspecies, relative to the organism strain prior to its transformation,wherein the decreased activated protein species is used by a pathwaythat limits the ability of the recombinant organism to produce apreferred solvent. In some variations the amount of decrease of theactivated protein species is 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%,50%, 55%, 60%, 65%, 70%, 75%, 80%, 90%, 95%, 100%, relative to theorganism strain prior to its transformation.

In one aspect of the invention, a recombinant organism species producesa particular solvent with increased efficiency. Increased efficiency ofsolvent production can be determined in any number of ways including butnot limited to: concentration (weight/volume) of solvent in fermentationmedium, yield (weight/weight) of solvent per amount of substrate, andrate of solvent formation (weight/volume/time).

In one aspect of the invention, a recombinant organism strain isscreened for an increased level of a particular solvent, relative to theorganism strain prior to its transformation. In some variations, arecombinant organism according to the present invention shows anincreased amount of a particular solvent relative to the organism strainprior to its transformation, wherein the amount of the particularsolvent is increased at least 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8,1.9, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, 3.6, 3.8, 4.0, 4.5, 5.0,5.5, 6.0, 6.5, 7.0, 7.5, 8.0, 8.5, 9.0, 9.5, 10, 15, 20, 40, 60, 80, or100-fold over that in the organism strain prior to its transformation.Where the concentration of the solvent in the organism strain prior toits transformation is 10 g/L, the concentration of the solvent in therecombinant solventogenic organism strain of the present invention is11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 24, 26, 28, 30, 32, 34, 36,38, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100 g/L. In someembodiments of the invention, the solvent concentration in a culture ofthe recombinant solventogenic organism strain is about 10, 20, 30, 40,50, or 60 g/L.

In some variations, a recombinant organism strain according to thepresent invention produces an increased yield of a particular solventper amount of the substrate, relative to the organism strain prior toits transformation. Where the yield of solvent in the organism strainprior to its transformation is about 20 g/g of substrate, a recombinantsolventogenic organism strain of the present invention produces yieldsof: 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 44, 48, 50, 52, 56, 60, 64,68, 72, 76, or 80 g solvent per g substrate. In some embodiments of theinvention, the yield from a culture of the recombinant solventogenicorganism strain is about 24, 30, 40, 50, or 60 g/g of substrate.

In some variations, a recombinant organism strain according to thepresent invention displays an increased rate of formation of aparticular solvent, relative to the organism strain prior to itstransformation. Where the rate of formation of solvent in the organismstrain prior to its transformation is about 0.2 g/L/hour of substrate arecombinant solventogenic organism strain of the present inventionproduces rates of solvent formation of: 0.24, 0.26, 0.28, 0.3, 0.32,0.34, 0.36, 0.38, 0.4, 0.44, 0.48, 0.52, 0.56, 0.6, 0.64, 0.68, 0.72,0.76, 0.8, 0.9, 1, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9, 2, 3, 4,8, or 12 g/L/hr. In some embodiments of the invention, the rate ofsolvent formation from a culture of the recombinant solventogenicorganism strain is about 0.24, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1,1.2, 1.4, 1.6, 1.8, 2.0, 2.2, 2.4, 2.6, 2.8, or 3.0 g/L/hour.

In some variations, a recombinant organism comprises an increased levelof a particular solvent, relative to the organism strain prior to itstransformation. In some variations, a recombinant organism comprises anincreased level of a particular solvent relative to the organism strainprior to its transformation, wherein the level of the particular solventis increased at least 0.05%, 0.1%, 0.15%, 0.2%, 0.25%, 0.3%, 0.35%,0.4%, 0.45%, 0.5%, 0.55%, 0.6%, 0.65%, 0.7%, 0.75%, 0.8%, 0.9%, 0.95%,1%, 1.1%, 1.2%, 1.3%, 1.4%, 1.5%, 1.6%, 1.7%, 1.8%, 1.9%, 2%, 2.1%,2.2%, 2.3%, 2.4%, 2.5%, 2.75%, 3%, 3.25%, 3.5%, 3.75%, 4%, 4.25%, 4.5%,or 5%. In some variations, a recombinant organism comprises an increasedlevel of a particular solvent relative to the organism strain prior toits transformation, wherein the level of the particular solvent isincreased at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 80%, 90%, 95%, 100%, 125%, 150%, 175%, 200%, 225%,250%, 275%, 300%., 325%, 350%, 375%, 400%, 425%, 450%, 475%, 500%, 600%,700%, 800%, 900%, or 1000%. In some variations, a recombinant organismcomprises an increased level of a particular solvent relative to theorganism strain prior to its transformation, wherein the level of theparticular solvent is increased at least 25%. In some variations, arecombinant organism comprises an increased level of a particularsolvent relative to the organism strain prior to its transformation,wherein the level of the particular solvent is increased at least 50%.In some variations, a recombinant organism comprises an increased levelof a particular solvent relative to the organism strain prior to itstransformation, wherein the level of the particular solvent is increasedat least 75%. In some variations, a recombinant organism comprises anincreased level of a particular solvent relative to the organism strainprior to its transformation, wherein the level of the particular solventis increased at least 100%. In some variations, a recombinant organismcomprises an increased level of a particular solvent relative to theorganism strain prior to its transformation, wherein the level of theparticular solvent is increased at least 200%. In some variations, arecombinant organism comprises an increased level of a particularsolvent relative to the organism strain prior to its transformation,wherein the level of the particular solvent is increased between0.05-500%. In some variations, a recombinant organism comprises anincreased level of a particular solvent relative to the organism strainprior to its transformation, wherein the level of the particular solventis increased between 0.05-300%. In some variations, a recombinantorganism comprises an increased level of a particular solvent relativeto the organism strain prior to its transformation, wherein the level ofthe particular solvent is increased between 0.5-500%. In somevariations, a recombinant organism comprises an increased level of aparticular solvent relative to the organism strain prior to itstransformation, wherein the level of the particular solvent is increasedbetween 5-500%. In some variations, a recombinant organism comprises anincreased level of a particular solvent relative to the organism strainprior to its transformation, wherein the level of the particular solventis increased between 100-500%. In some variations, a recombinantorganism comprises an increased level of a particular solvent relativeto the organism strain prior to its transformation, wherein the level ofthe particular solvent is increased between 10-100%. In some variations,a recombinant organism comprises an increased level of a particularsolvent relative to the organism strain prior to its transformation,wherein the level of the particular solvent is increased between500-1000%. In some variations, the solvent is butanol. In somevariations, the solvent is ethanol. In some variations, the solvent isacetone.

In some variations, an organism comprises an increased level of aparticular mRNA species. In some variations, a recombinant organismcomprises an increased level of a particular mRNA species, relative tothe organism strain prior to its transformation. In some variations, arecombinant organism comprises an increased level of a particular mRNAspecies relative to the organism strain prior to its transformation,wherein the level of the particular mRNA species is increased at least1.5-fold, 2-fold, 4-fold, 10-fold, 25-fold, 50-fold, or 100-foldrelative to the organism strain prior to its transformation. In somevariations, a recombinant organism comprises an increased level of aparticular mRNA species relative to the organism strain prior to itstransformation, wherein the level of the particular mRNA species isincreased at least 2-fold. In some variations, a recombinant organismcomprises an increased level of a particular mRNA species relative tothe organism strain prior to its transformation, wherein the level ofthe particular mRNA species is increased at least 5-fold. In somevariations, a recombinant organism comprises an increased level of aparticular mRNA species relative to the organism strain prior to itstransformation, wherein the level of the particular mRNA species isincreased at least 10-fold. In some variations, a recombinant comprisesan increased level of a particular mRNA species relative to the organismstrain prior to its transformation, wherein the level of the particularmRNA species is increased at least 15-fold. In some variations, arecombinant organism comprises an increased level of a particular mRNAspecies relative to the organism strain prior to its transformation,wherein the level of the particular mRNA species is increased at least20-fold. In some variations, a recombinant organism comprises anincreased level of a particular mRNA species relative to the organismstrain prior to its transformation, wherein the level of the particularmRNA species is increased at least 40-fold. In some variations, arecombinant organism comprises an increased level of a particular mRNAspecies relative to the organism strain prior to its transformation,wherein the level of the particular mRNA species is increased at least60-fold.

In some variations, an organism comprises an increased level of aparticular protein species. In some variations, a recombinant organismcomprises an increased level of a particular protein species, relativeto the organism strain prior to its transformation. In some variations,a recombinant organism comprises an increased level of a particularprotein species relative to the organism strain prior to itstransformation, wherein the level of the particular protein species isincreased at least 1.5-fold, 2-fold, 5-fold, 10-fold, 20-fold, 30-fold,40-fold, 50-fold, 60-fold, 80-fold, or 100-fold relative to the organismstrain prior to its transformation. In some variations, a recombinantorganism comprises an increased level of a particular protein speciesrelative to the organism strain prior to its transformation, wherein thelevel of the particular protein species is increased at least 1.5-fold.In some variations, a recombinant organism comprises an increased levelof a particular protein species relative to the organism strain prior toits transformation, wherein the level of the particular protein speciesis increased at least 5-fold. In some variations, a recombinant organismcomprises an increased level of a particular protein species relative tothe organism strain prior to its transformation, wherein the level ofthe particular protein species is increased at least 10-fold. In somevariations, a recombinant organism comprises an increased level of aparticular protein species relative to the organism strain prior to itstransformation, wherein the level of the particular protein species isincreased at least 20-fold. In some variations, a recombinant organismcomprises an increased level of a particular protein species relative tothe organism strain prior to its transformation, wherein the level ofthe particular protein species is increased at least 40-fold. In somevariations, a recombinant organism comprises an increased level of aparticular protein species relative to the organism strain prior to itstransformation, wherein the level of the particular protein species isincreased at least 60-fold. In some variations, a recombinant organismcomprises an increased level of a particular protein species relative tothe organism strain prior to its transformation, wherein the level ofthe particular protein species is increased at least 80-fold. In somevariations, a recombinant organism comprises an increased level of aparticular protein species relative to the organism strain prior to itstransformation, wherein the level of the particular protein species isincreased at least 100-fold.

In some variations, the amount of a particular protein species in theorganism strain prior to its transformation is 0.10 percent of the totalprotein in a cell. The amount of the particular protein species in therecombinant solventogenic organism strain is about 0.2, 0.5, 1.0, 2.0,4.0, 6.0, 8.0, 10.0 percent of the total protein in the cell.

In some variations, an organism comprises an increased level of aparticular activated protein species. In some variations, a recombinantorganism comprises an increased level of a particular activated proteinspecies, relative to the organism strain prior to its transformation. Insome variations, a recombinant organism comprises an increased level ofa particular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 1.5-fold, 2-fold,5-fold, 10-fold, 20-fold, 30-fold, 40-fold, 50-fold, 60-fold, 80-fold,or 100-fold relative to the organism strain prior to its transformation.In some variations, a recombinant organism comprises an increased levelof a particular activated protein species relative to the organismstrain prior to its transformation, wherein the level of the particularactivated protein species is increased at least 1.5-fold. In somevariations, a recombinant organism comprises an increased level of aparticular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 5-fold. In somevariations, a recombinant organism comprises an increased level of aparticular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 10-fold. In somevariations, a recombinant organism comprises an increased level of aparticular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 20-fold. In somevariations, a recombinant organism comprises an increased level of aparticular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 40-fold. In somevariations, a recombinant organism comprises an increased level of aparticular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 60-fold. In somevariations, a recombinant organism comprises an increased level of aparticular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 80-fold. In somevariations, a recombinant organism comprises an increased level of aparticular activated protein species relative to the organism strainprior to its transformation, wherein the level of the particularactivated protein species is increased at least 100-fold.

In some variations, the amount of a particular activated protein speciesin the organism strain prior to its transformation is 0.10 percent ofthe total protein in a cell. The amount of the particular activatedprotein species in the recombinant solventogenic organism strain isabout 0.2, 0.5, 1.0, 2.0, 4.0, 6.0, 8.0, 10.0 percent of the totalprotein in the cell.

Modifying Clostridia for Increasing Efficiency of Butanol Production.

U.S. Pat. No. 6,358,717 discloses a method of producing high levels ofbutanol using a fermentation process that employs a mutant strain ofClostridium beijerinckii. Clostridium beijerinckii BA101 (ATCC No.PTA-1550) is a hyper-butanol producing strain formed by mutagenesis ofthe wild type Clostridium beijerinckii NCIMB 8052. (Annous, B. A., andH. P. Blaschek. 1991. Isolation and characterization of Clostridiumacetobutylicum mutants with enhanced amylolytic activity. Appl. Environ.Microbiol. 57: 2544-2548; Formanek, J., R. Mackie, and H. P. Blaschek.1997. Enhanced butanol production by Clostridium beijerinckii BA101grown in semidefined P2 medium containing 6 percent maltodextrin orglucose. Appl. Environ. Microbiol. 63: 2306-2310.)

In one aspect of the invention, gene expression profiles of C.beijerinckii BA101 and the wild type C. beijerinckii NCIMB 8052 arecompared. Profiles of expression of solventogenic genes are comparedbetween the hyper-butanol producing C. beijerinckii BA101 and the wildtype C. beijerinckii NCIMB 8052. Typically, gene expression profiles arecompared using standard microarray techniques.

Microarrays comprising nucleic acid probes comprising the sequence ofone or more genes of C. beijerinckii BA101 or the wild type C.beijerinckii NCIMB 8052 are arrayed on a surface of the microarray. Thegenome of the wild type Clostridium beijerinckii 8052 is about 6.0 Mbpand the sequence is available at www.jgi.doe.gov (GenBank accessionnumber CP000721); thus probes corresponding to genes of the wild type C.beijerinckii NCIMB 8052 are readily obtained. Methods for fabricatingand using microarrays is found in U.S. Pat. No. 5,807,522, which isherein incorporated by reference. Instructions for constructingmicroarray hardware (e.g., arrayers and scanners) using commerciallyavailable parts can be found at http://cmgm.stanford.edu/pbr-own/and inCheung et al., 1999, Nat. Genet. Supplement 21: 15-19, which are hereinincorporated by reference. Additional discussions of microarraytechnology and protocols for preparing samples and performing microarrayexperiments are found in M. Schena (ed.), DNA Microarrays: A PracticalApproach, Oxford University Press, Oxford, UK, 1999. Descriptions of howto use an arrayer and the associated software are found athttp://cmgm.stanford.edu/pbrown/mguide/a-rrayerHTML/ArrayerDocs.html,which is herein incorporated by reference.

In a typical microarray experiment, a microarray is hybridized withdifferentially labeled RNA, DNA, or DNA populations derived from twodifferent samples. Most commonly RNA is isolated from cells or tissuesof interest and is reverse transcribed to yield DNA. Labeling is usuallyperformed during reverse transcription by incorporating a labelednucleotide in the reaction mixture. Although various labels can be used,most commonly the nucleotide is conjugated with the fluorescent dyes Cy3or Cy5. For example, Cy5-dUTP and Cy3-dUTP can be used. DNA derived fromone sample (representing, for example, a particular cell type or growthcondition) is labeled with one fluorophore while DNA derived from asecond sample (representing, for example, a different or mutant celltype, or growth condition) is labeled with the second fluorophore.Similar amounts of labeled material from the two samples arecohybridized to the microarray. In the case of a microarray experimentin which the samples are labeled with Cy5 (which fluoresces red) and Cy3(which fluoresces green), the primary data (obtained by scanning themicroarray using a detector capable of quantitatively detectingfluorescence intensity) are ratios of fluorescence intensity (red/green,R/G). These ratios represent the relative concentrations of DNAmolecules that hybridized to the DNA probes represented on themicroarray and thus reflect the relative expression levels of the mRNAcorresponding to each DNA probe/gene represented on the microarray.

Differential expression of genes, especially solventogenic genes, arecompared between C. beijerinckii BA101 and the wild type C. beijerinckiiNCIMB 8052. In some embodiments, expression profiles are correlated withsolvent production and butanol production phases, respectively of C.beijerinckii BA101, C. beijerinckii NCIMB 8052 or both. Sets of genesthat are differentially expressed between the wild type andhyper-butanol mutant are identified. Genes in the hyper-butanol mutantC. beijerinckii BA101 show increased or decreased expression relative togenes of the wild type C. beijerinckii NCIMB 8052. In one aspect thesegenes are involved in one or more solvent production-related pathwayssuch as solventogenesis, chemotaxis, motility, sporulation and sugartransport.

In one aspect of the invention, one or more of these genes areidentified and their expression profiles corresponding to ahyper-butanol producing state is replicated in a Clostridium, preferablyin a Clostridium beijerinckii. This can be accomplished in a number ofways including, but not limited to, transforming a microorganism such asclostridia with the gene under the control of a constitutive orinducible promoter. The promoter is designed to replicate the increasedor decreased gene expression (relative to wild type) observed in thehyper-butanol producing mutant. In one aspect the organism transformedwith a wild type gene from Clostridium beijerinckii NCIMB 8052, whosegenetic (DNA) sequence is publicly available.

In one aspect of the invention, the sequences of Clostridiumbeijerinckii NCIMB 8052 and hyper-butanol producing Clostridiumbeijerinckii BA101 are compared. Clostridium beijerinckii BA101 ispublicly available (ATCC No. PTA-1550) and may be sequenced usingmethods known to those of skill in the art. In some variations, arecombinant organism is transformed with one or more genes fromClostridium beijerinckii BA101 that has a sequence different from thecorresponding gene in Clostridium beijerinckii NCIMB 8052. Where theexpression of the gene is altered in BA101 relative to the wild-type, asuitable promoter is operably linked to the gene sequence prior totransformation. The promoter is able to be used to replicate the geneexpression profile in BA101 in the recombinant organism.

In one aspect of the invention, the genes related to the solventproductions pathways identified by this analysis include homologousgenes with at least 70, 75, 80, 83, 85, 90, 95, 97, 99 or 100% homologywith the known sequence of a gene in wild type C. beijerinckii NCIMB8052.

In another embodiment of the invention, homologous polynucleotides areidentified by the ability to hybridize under moderate to high stringencyconditions to a polynucleotide sequence provided herein, or a fragmentthereof, or a complementary sequence thereof. Hybridization techniquesare well known in the art of molecular biology. High stringencyconditions are known in the art. See, for example, Maniatis et al.,Molecular Cloning: A Laboratory Manual, 2d Edition, 1989, and ShortProtocols in Molecular Biology, ed. Ausubel, et al. Stringent conditionsare sequence-dependent and will be different in different circumstances.Longer sequences hybridize specifically at higher temperatures. Anextensive guide to the hybridization of nucleic acids is found inTijssen, Techniques in Biochemistry and Molecular Biology—Hybridizationwith Nucleic Acid Probes, “Overview of principles of hybridization andthe strategy of nucleic acid assays” (1993). Generally, stringentconditions are selected to be about 5-10° C. lower than the thermalmelting point (T_(m)) for the specific sequence at a defined ionicstrength pH. The T_(m) is the temperature (under defined ionic strength,pH and nucleic acid concentration) at which 50% of the probescomplementary to the target hybridize to the target sequence atequilibrium (as the target sequences are present in excess, at T_(m),50% of the probes are occupied at equilibrium). Stringent conditionswill be those in which the salt concentration is less than about 1.0 Msodium ion, typically about 0.01 to 1.0 M sodium ion concentration (orother salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C. for short probes (e.g. 10 to 50 nucleotides) and at least about 60°C. for longer probes (e.g. greater than 50 nucleotides). In anotherembodiment, less stringent hybridization conditions are used. Forexample, moderate or low stringency conditions may be used, as are knownin the art. (See Maniatis and Ausubel, supra, and Tijssen, supra). Forpurposes of illustration, suitable moderately stringent conditions fortesting the hybridization of a polynucleotide of this invention withother polynucleotides include prewashing in a solution of 5×SSC (“salinesodium citrate”; 9 mM NaCl, 0.9 mM sodium citrate), 0.5% SDS, 1.0 mMEDTA (pH 8.0); hybridizing at 50-60° C., 5×SSC, overnight; followed bywashing twice at 65° C. for 20 minutes with each of 2×, 0.5× and 0.2×SSCcontaining 0.1% SDS. One skilled in the art will understand that thestringency of hybridization can be readily manipulated, such as byaltering the salt content of the hybridization solution and/or thetemperature at which the hybridization is performed. For example, inanother embodiment, suitable highly stringent hybridization conditionsinclude those described above, with the exception that the temperatureof hybridization is increased, e.g., to 60-65° C., or 65-70° C.Stringent conditions may also be achieved with the addition ofdestabilizing agents such as formamide.

Identification of homologous genes can also be performed by optimalalignment of sequences for comparison to analyze sequence identity(homology) known in the art. Homology in this context means sequencesimilarity or identity, with identity being preferred. This homology isdetermined using standard techniques known in the art, including, butnot limited to, the local homology algorithm of Smith & Waterman, Adv.Appl. Math. 2: 482 (1981), by the homology alignment algorithm ofNeedleman & Wunsch, J. Mol. Biol. 48: 443 (1970), by the search forsimilarity method of Pearson & Lipman, PNAS USA 85: 2444 (1988), bycomputerized implementations of these algorithms (GAP, BESTFIT, FASTA,and TFASTA in the Wisconsin Genetics Software Package, Genetics ComputerGroup, 575 Science Drive, Madison, Wis.), the Best Fit sequence programdescribed by Devereux et al., Nucl. Acid Res. 12: 387-395 (1984),preferably using the default settings, or by inspection. One example ofa useful algorithm is PILEUP. PILEUP creates a multiple sequencealignment from a group of related sequences using progressive, pairwisealignments. It can also plot a tree showing the clustering relationshipsused to create the alignment. PILEUP uses a simplification of theprogressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351-360 (1987); the method is similar to that described by Higgins &Sharp CABIOS 5: 151-153 (1989). Useful PILEUP parameters include adefault gap weight of 3.00, a default gap length weight of 0.10, andweighted end gaps. Another example of a useful algorithm is the BLAST(Basic Local Alignment Search Tool) algorithm, described in Altschul etal., J. Mol. Biol. 215, 403-410, (1990) and Karlin et al., PNAS USA 90:5873-5787 (1993). A particularly useful BLAST program is the WU-BLAST-2program which was obtained from Altschul et al., Methods in Enzymology,266: 460-480 (1996); http://blast.wustl.edu/]. WU-BLAST-2 uses severalsearch parameters, most of which are set to the default values. Theadjustable parameters are set with the following values: overlap span=1,overlap fraction=0.125, word threshold (T)=11. The HSP S and HSP S2parameters are dynamic values and are established by the program itselfdepending upon the composition of the particular sequence andcomposition of the particular database against which the sequence ofinterest is being searched; however, the values may be adjusted toincrease sensitivity. A percent amino acid sequence identity value isdetermined by the number of matching identical residues divided by thetotal number of residues of the “longer” sequence in the aligned region.The “longer” sequence is the one having the most actual residues in thealigned region (gaps introduced by WU-Blast-2 to maximize the alignmentscore are ignored). Thus, “percent (%) nucleic acid sequence identity”is defined as the percentage of nucleotide residues in a candidatesequence that are identical with the nucleotide residues of a particularnucleic acid. A preferred method utilizes the BLASTN module ofWU-BLAST-2 set to the default parameters, with overlap span and overlapfraction set to 1 and 0.125, respectively.

The nucleic acids of the present invention that are identified byaltered expression or nucleotide sequence in the hyper-butanol producingclostridia can be used to isolate nucleic acids encoding homologousproteins from other strains of the same or other species andmicroorganisms, such as Clostridia, Escherichia, Sachharomyces, etc.Isolation of homologous genes using sequence-dependent protocols is wellknown in the art. Examples of sequence-dependent protocols include, butare not limited to, methods of nucleic acid hybridization, and methodsof DNA and RNA amplification as exemplified by various uses of nucleicacid amplification technologies (e.g., polymerase chain reaction, ligasechain reaction). For example, genes encoding homologous proteins, eitheras DNA's or genomic DNA's, could be isolated directly by using all or aportion of the nucleic acids of the present invention as DNAhybridization probes to screen DNA or genomic libraries from any desiredorganism employing methodology well known to those skilled in the art.Methods for forming such libraries are well known in the art (Sambrooket al., Molecular Cloning: A Laboratory Manual; Cold Spring HarborLaboratory Press, Cold Spring Harbor, 1989).

Nucleic acids of interest may also be synthesized, either completely orin part, especially where it is desirable to provide host-preferredsequences, by well-known techniques. See, e.g., Carruthers et al. (ColdSpring Harbor Symp. Quant. Biol. 47: 411-418, 1982) and Adams et al. (J.Am. Chem. Soc. 105: 661, 1983). Thus, all or a portion of the nucleicacids of the present invention may be synthesized using codons preferredby a selected host.

Genes and homologs and variants thereof that are identified as having arole in hyper-production of butanol can be used for transforming hostspecies or organisms for the high efficiency production of butanol. Inone aspect, the nucleic acids used for transformation comprise thesequence of the gene as well as an operably linked constitutive orinducible promoter that can be used to regulate expression of the gene.Specific examples of methods for modifying clostridia for increasingefficiency of butanol production are provided infra.

Methods of Preparing Substrates

In addition to conventional starch (maize, wheat, millet, rye, etc.) orsugar (molasses) substrates saccharolytic clostridia are able to utilizemany different carbohydrates. (See Jones and Woods, 1986, supra.)Solvent production starting materials such as biomass, plant-based,cellulosic, lignocellulosic or hemicellulosic materials may be directlyentered into the solvent production process. However, often suchmaterials are pretreated to convert lignocellulosic biomass into a formwhich is more accessible to cellulolytic and fermentation processes.Pretreatment typically includes one or more of increasing the surfacearea to volume ratio by, for example comminution; steam treatment, acidhydrolysis, or enzymatic treatment. Those of skill in the art arefamiliar with these and other pretreatment methods.

Methods of Processing Cellulose to Sugars

Cellulosic and hemicellulosic materials may be converted to downstreamproducts such as fermentable sugars by various methods. In somevariations, biomass, lignocellulosic, or cellulosic materials areconverted to downstream products such as fermentable sugars via a methodwhich does not require living bacteria, yeast, or other organisms.

In some variations, biomass, lignocellulosic, or cellulosic materialsare converted to downstream products such as fermentable sugars via amethod which utilizes living bacteria, yeast, or other organisms.

In some variations, any organism capable of processing biomass,lignocellulosic, or cellulosic materials to one or more usefuldownstream products, including but not limited to fermentable sugars, isused in the methods described herein. In some variations, any organismcapable of processing cellulose to one or more useful downstreamproducts, including but not limited to fermentable sugars, is used inthe methods described herein.

In some variations, a cellulolytic yeast, bacteria or other organism,including but not limited to Clostridia, Saccharomyces, or Escherichiastrains, are naturally or through genetic manipulation made capable ofprocessing biomass, lignocellulosic, or cellulosic materials to one ormore useful downstream products, including but not limited tofermentable sugars.

In some variations, a solventogenic organism is transformed with one ormore genes or regulatory sequences controlling expression of a generelating to the conversion of biomass, lignocellulosic, or cellulosicmaterials to one or more useful downstream products, including but notlimited to fermentable sugars.

In some variations, a solventogenic organism is transformed with one ormore heterologous genes or heterologous regulatory sequences controllinga gene relating to the conversion of biomass, lignocellulosic, orcellulosic materials to one or more useful downstream products,including but not limited to fermentable sugars.

In some variations, a solventogenic organism is transformed with one ormore genes relating to activation or inactivation of a gene productinvolved in the conversion of biomass, lignocellulosic, or cellulosicmaterials to one or more useful downstream products, including but notlimited to fermentable sugars.

In some variations, a solventogenic organism is transformed with one ormore cellulolytic genes. In some variations, a solventogenic organism istransformed with one or more genes involved in generating a functionalcellulosome complex. In some variations, a solventogenic organism istransformed with all of the genes involved in a cellulosome complex.

In some variations, a solventogenic organism is transformed with one ormore secretable cellulolytic genes. In some variations, anon-solventogenic organism is transformed with one or more secretablecellulolytic genes. In some variations, a solventogenic organism istransformed with one or more secretable cellulolytic genes. In somevariations, a solventogenic organism is transformed with all of thesecretable cellulolytic genes necessary to convert biomass,lignocellulosic, or cellulosic materials to one or more usefuldownstream products, including but not limited to fermentable sugars.

In some variations, a solventogenic organism is transformed with one ormore cellulolytic genes. In some variations, a solventogenic organism istransformed with one or more genes involved in generating a functionalcellulosome complex. In some variations, a solventogenic organism istransformed with all of the genes involved in a cellulosome complex.

In some variations, a solventogenic organism is transformed with one ormore genes encoding one or more enzymes that cut at random at internalamorphous sites in a cellulose polysaccharide chain. In some variations,a solventogenic organism is transformed with one or more genes encodingone or more endoglucanases or 1,4-beta-D-glucan-4-glucanohydrolases.

In some variations, a solventogenic organism is transformed with one ormore genes encoding one or more enzymes that process reducing ornonreducing ends of cellulose polysaccharide chains to hexoses such asglucose, or cellobiose. In some variations, a solventogenic organism istransformed with one or more genes encoding one or more exoglucanases.In some variations, a solventogenic organism is transformed with one ormore genes encoding one or more 1,4-beta-D-glucan glucanohydrolases,cellodextrinases, 1,4-beta-D-glucan cellobiohydrolases, orcellobiohydrolases.

In some variations, a solventogenic organism is transformed with one ormore genes encoding one or more beta-glucosidases or beta-glucosideglucohydrolases.

In some variations, a solventogenic organism is transformed with one ormore genes encoding one or more scaffoldin-type proteins.

In some variations, a solventogenic organism is transformed with one ormore genes or regulatory sequences which decrease or impair the activityof one or more pathways which decrease or impair the solventogenicpotential of a solventogenic organism. In some variations, asolventogenic organism is transformed with one or more heterologousgenes or heterologous regulatory sequences which decrease or impair theactivity of one or more pathways which decrease or impair thesolventogenic potential of a solventogenic organism. In some variations,a solventogenic organism is transformed with one or more genes orregulatory sequences which decrease or impair the activity of one ormore pathways which decrease or impair the solventogenic potential of aClostridium strain, including but not limited to C. beijerinckii or C.beijerinckii BA101.

Methods of Generating Solvents from Sugars

Cellulosic materials are typically converted into a mixture of hexosesugars, such as glucose and mannose, and pentose sugars, such as xyloseand arabinose. These sugars may then be acted upon to generate one ormore solvents.

In some variations, the organisms described herein are optimized toferment one or more hexose or pentose sugars to solvents, for examplebutanol, ethanol, or acetone. In some variations, the organismsdescribed herein are optimized to ferment all major hexose or pentosesugars to solvents. In some variations, the organisms described hereinare optimized to ferment one or more of glucose, mannose, xylose orarabinose: In some variations, the organisms described herein areoptimized to ferment glucose. In some variations, the organismsdescribed herein are optimized to ferment mannose. In some variations,the organisms described herein are optimized to ferment xylose. In somevariations, the organisms described herein are optimized to fermentarabinose.

In some variations the organism that converts one or more hexose orpentose sugars to a solvent, including but not limited to butanol, isalso capable of converting cellulosic material to hexose or pentosesugars, with or without pretreatment.

In some variations the organism that converts one or more hexose orpentose sugars to a solvent, including but not limited to butanol, isnot capable of converting cellulosic material to hexose or pentosesugars, with or without pretreatment.

In some variations the process utilizing an organism that converts oneor more hexose or pentose sugars to a solvent, including but not limitedto butanol, includes simultaneous or sequential use of a second organismor strain that is capable of converting cellulosic material to hexose orpentose sugars, with or without pretreatment.

In some variations, the organisms described herein are optimized toferment one or more hexose or pentose sugars by increasing orfacilitating the organism's use of favored pathways. In some variations,the organisms described herein are optimized to ferment one or more ofglucose, mannose, xylose or arabinose by increasing or facilitating theorganism's use of favored pathways.

In some variations, the organisms described herein are optimized toferment one or more hexose or pentose sugars by decreasing or impairinguse of pathways which decrease or impair production of a solvent ofinterest. In some variations, the organisms described herein areoptimized to ferment one or more of glucose, mannose, xylose orarabinose by decreasing or impairing use of pathways which decrease orimpair production of a solvent of interest.

In some variations, an organism described herein is transformed with oneor more genes involved in the metabolic pathway of a particular hexoseor pentose sugar. In some variations, an organism described herein istransformed with all genes involved in the metabolic pathway of aparticular hexose or pentose sugar. In some variations, an organismdescribed herein is transformed with one or more genes involved in themetabolic pathway of glucose. In some variations, an organism describedherein is transformed with all genes involved in the metabolic pathwayof glucose. In some variations, an organism described herein istransformed with one or more genes involved in the metabolic pathway ofmannose. In some variations, an organism described herein is transformedwith all genes involved in the metabolic pathway of mannose. In somevariations, an organism described herein is transformed with one or moregenes involved in the metabolic pathway of xylose. In some variations,an organism described herein is transformed with all genes involved inthe metabolic pathway of xylose. In some variations, an organismdescribed herein is transformed with one or more genes involved in themetabolic pathway of arabinose. In some variations, an organismdescribed herein is transformed with all genes involved in the metabolicpathway of arabinose.

In some variations, an organism described herein is transformed with oneor more genes involved in the metabolic pathway of a particular hexoseor pentose sugar from a bacteria. In some variations, an organismdescribed herein is transformed with one or more genes involved in themetabolic pathway of a particular hexose or pentose sugar from aNeurospora strain, including but not limited to N. crassa.

In some variations, the titer, yield and productivity of solventproduction is increased by optimizing the various metabolic pathwaysinvolved in the biosynthesis of one or more solvents of interest,including but not limited to butanol, ethanol, and acetone. In somevariations, the titer, yield and productivity of butanol production isincreased by optimizing the various metabolic pathways involved in thebiosynthesis of butanol. In some variations, metabolic flux analysis isused to identify the rate-limiting steps in solvent synthesis in anorganism described herein, including but not limited to a Clostridium orS. cerevisiae strain.

By way of nonlimiting example, for a linear pathway, the level of finalproduct is related to the overall flux through the pathway. An optimizedsolvent biosynthetic pathway should have increased overall flux throughthe pathway without significant accumulation of pathway intermediates.Various analytical instruments may be used to determine theconcentrations of key metabolites in the metabolic pathways involved inthe biosynthesis of the solvent at fermentation conditions and identifythe rate-limiting enzymes. Non-limiting examples of analyticalinstruments include GC-MS, HPLC-MS, HPLC (stand alone), Piezorrayrobotic printer (non-contact microarray printing onto membranes, plates,and slides), UV/visible/fluorescence microplate reader, andchemiluminometer microplate reader. To trace the metabolites, C-14 basedisotopic labeling methods in combination with either LC-MS or NMR may beused.

Once the rate-limiting enzymes are identified in an organism describedherein, overexpression of the one or more genes limiting the overallflux may be used to determine its effect on the concentrations ofpathway intermediates and the final solvent product. If the productconcentration is increased, then the overexpressed gene or genes areindeed positively correlated with solvent production. Non-limitingexamples of strategies to balance gene expression include manipulationof promoter strength, ribosomal binding site (RBS) strength, genelocation in an operon, and mRNA stability.

The effect of various sporulation, motility, and sugar transport genesmay be similarly evaluated. For example, increasing or decreasing theexpression of one or more genes relating to sporulation, motility, andsugar transport may be used to determine their effect on theconcentrations of pathway intermediates and the final solvent product.If the product concentration is increased, then the gene or genes withincreased or decreased expression are correlated with solventproduction. Non-limiting examples of strategies to balance geneexpression include manipulation of promoter strength, ribosomal bindingsite (RBS) strength, gene location in an operon, and mRNA stability.

Solventogenic Genes

Acid concentration and reducing state are also known to influence theproduction of solvents and hence, impact the expression ofsolvent-related genes in Clostridium. Genes involved in solventproduction and butanol production are identified in FIG. 9.

As demonstrated in FIG. 4, alcohol dehydrogenase (Adh), butyryl-CoAdehydrogenase (Bcd) and butyrate kinase (Buk) are expressed at altered(higher or lower) levels during the solventogenic stage in BA101compared with the wild-type C. beijerinckii strain.

In some variations, an organism described herein is optimized toincrease production of an enzyme in the solventogenic pathway. In somevariations, an organism described herein is transformed with a geneencoding an enzyme in the solventogenic pathway. In some variations anorganism described herein is transformed with a gene encoding an enzymein the solventogenic pathway to overexpress the enzyme.

In some variations, an organism described herein is optimized toincrease production of all of the enzymes described herein in thebutanol solventogenic pathway. In some variations, an organism describedherein is transformed with all of the enzymes described herein in thebutanol solventogenic pathway. In some variations an organism describedherein is transformed with a gene encoding all of the enzymes describedherein in the butanol solventogenic pathway to overexpress the enzymes.

Alcohol dehydrogenase (Adh) encodes an important terminal enzymerequired for alcohol production. Thus, increased Adh expression maydirectly contribute to elevated butanol synthesis in BA101. In somevariations, an organism described herein is optimized to increaseproduction of Adh. In some variations, an organism described herein istransformed with an Adh gene. In some variations an organism describedherein is transformed with an Adh gene to overexpress Adh. In somevariations, an organism described herein is transformed with an Adh genefrom a microbial organism to overexpress Adh. In some variations, anorganism described herein is transformed with an Adh gene from aClostridium sp. to overexpress Adh. In some variations, an organismdescribed herein is transformed with an Adh gene from Clostridiumbeijerinckii to overexpress Adh. In some variations, an organismdescribed herein is transformed with a nucleic acid which results in anincrease in expression of the Adh gene whose DNA sequence is shown inFIG. 10. In some variations, an organism described herein is transformedwith an Adh gene whose DNA sequence is shown in FIG. 10 to overexpressAdh.

In some variations, an organism described herein is transformed with anAdh gene whose DNA sequence is at least 60-100% identical to the DNAsequence shown in FIG. 10 or complement thereof. In some variations, anorganism described herein is transformed with an Adh gene whose DNAsequence is at least 80-100% identical to the DNA sequence shown in FIG.10 or complement thereof. In some variations, an organism describedherein is transformed with an Adh gene whose DNA sequence is at least90-100% identical to the DNA sequence shown in FIG. 10 or complementthereof. In some variations, an organism described herein is transformedwith an Adh gene whose DNA sequence is at least 60, at least 65, atleast 70, at least 75, at least 80, at least 85, at least 90, at least95, or 100% identical to the DNA sequence shown in FIG. 10 or complementthereof. In some variations, an organism described herein is transformedwith an Adh gene whose DNA sequence is at least 80% identical to the DNAsequence shown in FIG. 10 or complement thereof. In some variations, anorganism described herein is transformed with an Adh gene whose DNAsequence is at least 85% identical to the DNA sequence shown in FIG. 10or complement thereof. In some variations, an organism described hereinis transformed with an Adh gene whose DNA sequence is at least 90%identical to the DNA sequence shown in FIG. 10 (SEQ ID NO: 1) orcomplement thereof. The Clostridium beijerinckii NCIMB 8052 publishedgenome identifies this adh gene as Cbei_(—)2181.

The C. beijerinckii NCIMB 8052 published genome identifies the adh geneshown in FIG. 10 as Cbei_(—)2181 (SEQ ID NO: 1). NCBI BLAST searchagainst the C. beijerinckii NCIMB 8052 genome revealed another C.beijerinckii NCIMB 8052 gene that is a close homolog of Cbei_(—)2181 atboth the DNA sequence and the protein sequence levels. The DNA sequence(SEQ ID NO: 14) is shown in FIG. 22A and predicted amino acid sequence(SEQ ID NO: 15) of Cbei_(—)1722 is shown in FIG. 22B.

At the DNA level the Cbei_(—)1722 adh gene shows 90% identity toCbei_(—)2181 with 1% gaps in the alignment. At the protein level theCbei_(—)1722 adh protein shows 93% amino acid identity to Cbei_(—)2181,with 97% similarity and zero gaps. The DNA and protein alignments bothshow an “Expect value” of zero, suggesting the two enzymes are eitherfunctionally equivalent, or nearly so. The Cbei_(—)1722 adh gene isannotated at an “iron-containing alcohol dehydrogenase”. Multipleisozymes of the class of adh enzymes are known to exist insolvent-forming Clostridium species and are known to be induced orde-repressed near the onset of solvent formation (Walter K A, Bennett GN, Papoutsakis E T; Molecular characterization of two Clostridiumacetobutylicum ATCC 824 butanol dehydrogenase isozyme genes; J.Bacteriol. 1992 November; 174(22):7149-58). It is postulated thatCbei_(—)1722 could be used in the same manner as the Cbei_(—)2181 adhgene.

Butyryl-CoA dehydrogenase (Bcd) catalyzes the formation of butyryl-CoA,an immediate precursor for butanol. Higher Bcd expression in BA101 maylead to increased butyryl-CoA production, which in turn may improve theformation of butanol. In some variations, an organism described hereinis optimized to increase production of Bcd. In some variations, anorganism described herein is transformed with a Bcd gene. somevariations an organism described herein is transformed with a Bcd geneto overexpress Bcd. In some variations, an organism described herein istransformed with a Bcd gene from a microbial organism to overexpressBcd. In some variations, an organism described herein is transformedwith a Bcd gene from a Clostridium sp. to overexpress Bcd. In somevariations, an organism described herein is transformed with a Bcd genefrom Clostridium beijerinckii to overexpress Bcd. In some variations, anorganism described herein is transformed with a nucleic acid whichresults in an increase in expression of the Bcd gene whose DNA sequenceis shown in FIG. 11. In some variations, an organism described herein istransformed with a Bcd gene whose DNA sequence is shown in FIG. 11 (SEQID NO: 2) to overexpress Bcd. The Clostridium beijerinckii NCIMB 8052published genome identifies this bcd gene as Cbei_(—)2035.

In some variations, an organism described herein is transformed with aBcd gene whose DNA sequence is at least 60-100% identical to the DNAsequence shown in FIG. 11 or complement thereof. In some variations, anorganism described herein is transformed with a Bcd gene whose DNAsequence is at least 80-100% identical to the DNA sequence shown in FIG.11 or complement thereof. In some variations, an organism describedherein is transformed with a Bcd gene whose DNA sequence is at least90-100% identical to the DNA sequence shown in FIG. 11 or complementthereof. In some variations, an organism described herein is transformedwith a Bcd gene whose DNA sequence is at least 60, at least 65, at least70, at least 75, at least 80, at least 85, at least 90, at least 95, or100% identical to the DNA sequence shown in FIG. 11 or complementthereof. In some variations, an organism described herein is transformedwith a Bcd gene whose DNA sequence is at least 80% identical to the DNAsequence shown in FIG. 11 or complement thereof. In some variations, anorganism described herein is transformed with a Bcd gene whose DNAsequence is at least 85% identical to the DNA sequence shown in FIG. 11or complement thereof. In some variations, an organism described hereinis transformed with a Bcd gene whose DNA sequence is at least 90%identical to the DNA sequence shown in FIG. 11 or complement thereof.

The C. beijerinckii NCIMB 8052 published genome identifies the bcd geneshown in FIG. 11 as Cbei_(—)2035 (SEQ ID NO:2). Other genes identifiedin the C. beijerinckii NCIMB 8052 published genome that are closehomologs of the bcd gene Cbei_(—)2035 (SEQ ID NO:2) includeCbei_(—)0322. The DNA sequence of Cbei_(—)0322 (SEQ ID NO: 12) shown inFIG. 21A and the protein sequence of Cbei_(—)0322 (SEQ ID NO: 13) shownin FIG. 21B.

Cbei_(—)0322 shows 98% identity to Cbei_(—)2035 at the DNA level and 98%identity at the protein sequence level, with no gaps. The close homologysuggests that gene Cbei_(—)0322 could show Bcd activity. Cbei_(—)0322 isannotated as a “acyl-CoA dehydrogenase domain protein” which isconsistent with its being a bcd gene. Cbei_(—)2035 (SEQ ID NO:2) is alsoannotated as “acyl-CoA dehydrogenase domain protein” in the GenBankrecord. While it is possible that the native role of the Cbei_(—)0322protein may be in a pathway other than solvent production, such as forinstance the metabolism of other fatty acids, its close homology toCbei_(—)2035 suggests that even if that were true, it could be used as afunctional Bcd gene under the control of an appropriate promoter.

Butyrate kinase (Buk) is a key enzyme in butyrate synthesis. IncreasedBuk activity in BA101 may allow the generation of higher amounts ofbutyrate, which can then be converted into butyryl-CoA and further intobutanol. In some variations, an organism described herein is optimizedto increase production of Buk. In some variations, an organism describedherein is transformed with a Buk gene. In some variations an organismdescribed herein is transformed with a Buk gene to overexpress Buk. Insome variations, an organism described herein is transformed with a Bukgene from a microbial organism to overexpress Buk. In some variations,an organism described herein is transformed with a Buk gene from aClostridium sp. to overexpress Buk. In some variations, an organismdescribed herein is transformed with a Buk gene from Clostridiumbeijerinckii to overexpress Buk. In some variations, an organismdescribed herein is transformed with a nucleic acid which results in anincrease in expression of the Buk gene whose DNA sequence is shown inFIG. 12. In some variations, an organism described herein is transformedwith a Buk gene whose DNA sequence is shown in FIG. 12 to overexpressBuk.

In some variations, an organism described herein is transformed with aBuk gene whose DNA sequence is at least 60-100% identical to the DNAsequence shown in FIG. 12 or complement thereof. In some variations, anorganism described herein is transformed with a Buk gene whose DNAsequence is at least 80-100% identical to the DNA sequence shown in FIG.12 or complement thereof. In some variations, an organism describedherein is transformed with a Buk gene whose DNA sequence is at least90-100% identical to the DNA sequence shown in FIG. 12 or complementthereof. In some variations, an organism described herein is transformedwith a Buk gene whose DNA sequence is at least 60, at least 65, at least70, at least 75, at least 80, at least 85, at least 90, at least 95, or100% identical to the DNA sequence shown in FIG. 12 or complementthereof. In some variations, an organism described herein is transformedwith a Buk gene whose DNA sequence is at least 80% identical to the DNAsequence shown in FIG. 12 or complement thereof. In some variations, anorganism described herein is transformed with a Buk gene whose DNAsequence is at least 85% identical to the DNA sequence shown in FIG. 12or complement thereof. In some variations, an organism described hereinis transformed with a Buk gene whose DNA sequence is at least 90%identical to the DNA sequence shown in FIG. 12 or complement thereof.

In some variations, an organism described herein is optimized toincrease expression of any one or more of Adh, Bcd, or Buk. In somevariations, an organism described herein is transformed with a genesencoding any one or more of Adh, Bcd, or Buk. In some variations anorganism described herein is transformed with genes encoding each ofAdh, Bcd, and Buk to overexpress Adh, Bcd, and Buk. In some variationsan organism described herein is transformed with a nucleic acid whichincreases expression of any one or more of Adh, Bcd, or Buk.

Genes of Solvent Production Pathway

As demonstrated in FIG. 8, expression of aceto-acetylCoA:acetate-butyrate CoA transferase subunit α/β (CtfA/B) andacetoacetate decarboxylase (Adc) was highly activated at the onset ofsolventogenic phase in BA101 and the wild-type strain. Changes inexpression levels were much smaller for thiolase (Thl),3-hydroxybutyryl-CoA dehydrogenase (Hcd) and crotonase (Crt) in BA101and the wild-type strain.

Despite the somewhat comparable expression kinetics of CtfA/B, Adc, Thl,Hcd and Crt in the BA101 strain relative to the wild type parent,altering (increasing or decreasing) the expression of these genes mayprove useful in increasing solvent production in the organisms describedherein.

In some variations, an organism described herein is optimized toincrease production of one or more solvents by changing the expressionof any one or more of CtfA/B, Adc, Thl, Hcd and Crt. In some variations,an organism described herein is optimized to increase production of oneor more solvents by increasing the expression of one or more of CtfA/B,Adc, Thl, Hcd and Crt. In some variations, an organism described hereinis optimized to increase production of one or more solvents bydecreasing the expression of one or more of CtfA/B, Adc, Thl, Hcd andCrt. In some variations, an organism described herein is transformedwith genes encoding any one or more of CtfA/B, Adc, Thl, Hcd and Crt.

In some variations, an organism described herein is optimized todecrease production of one or more gene products which compete with orare otherwise detrimental to the production of solvents. In somevariations an organism described herein is transformed with a nucleicacid to decrease or impair expression of one or more gene products whichcompete with or are otherwise detrimental to the production of solvents.

In some variations an organism described herein is transformed with anucleic acid to decrease or impair expression of Adc. In some variationsan organism described herein is transformed with a nucleic acid toincrease expression of Adc. In some variations, an organism describedherein is transformed with an Adc gene from a microbial organism tooverexpress Adc. In some variations, an organism described herein istransformed with an Adc gene from a Clostridium sp. to overexpress Adc.In some variations, an organism described herein is transformed with anAdc gene from Clostridium beijerinckii to overexpress Adc.

In some variations, an organism described herein is transformed with anAdc gene whose DNA sequence is at least 60-100% identical to that of theClostridium beijerinckii NCIMB 8052 gene. In some variations, anorganism described herein is transformed with an Adc gene whose DNAsequence is at least 60-100% identical to that of the Clostridiumbeijerinckii BA101 gene. In some variations, an organism describedherein is transformed with an Adc gene whose DNA sequence is at least60, at least 65, at least 70, at least 75, at least 80, at least 85, atleast 90, at least 95, or 100% identical to that of the Clostridiumbeijerinckii NCIMB 80 gene. In some variations, an organism describedherein is transformed with an Adc gene whose DNA sequence is at least60, at least 65, at least 70, at least 75, at least 80, at least 85, atleast 90, at least 95, or 100% identical to that of the Clostridiumbeijerinckii BA101 gene.

In some variations an organism described herein is transformed with anucleic acid to decrease or impair expression of CtfA/B. In somevariations an organism described herein is transformed with a nucleicacid to increase expression of CtfA/B. In some variations, an organismdescribed herein is transformed with a CtfA/B gene from a microbialorganism to overexpress CtfA/B. In some variations, an organismdescribed herein is transformed with a CtfA/B gene from a Clostridiumsp. to overexpress CtfA/B. In some variations, an organism describedherein is transformed with a CtfA/B gene from Clostridium beijerinckiito overexpress CtfA/B.

In some variations, an organism described herein is transformed with aCtfA/B gene whose DNA sequence is at least 60-100% identical to that ofthe Clostridium beijerinckii NCIMB 8052 gene. In some variations, anorganism described herein is transformed with a CtfA/B gene whose DNAsequence is at least 60-100% identical to that of the Clostridiumbeijerinckii BA101 gene. In some variations, an organism describedherein is transformed with a CtfA/B gene whose DNA sequence is at least60, at least 65, at least 70, at least 75, at least 80, at least 85, atleast 90, at least 95, or 100% identical to that of the Clostridiumbeijerinckii NCIMB 80 gene. In some variations, an organism describedherein is transformed with a CtfA/B gene whose DNA sequence is at least60, at least 65, at least 70, at least 75, at least 80, at least 85, atleast 90, at least 95, or 100% identical to that of the Clostridiumbeijerinckii BA101 gene.

In some variations an organism described herein is transformed with anucleic acid to decrease or impair expression of a gene product leadingto production of a solvent other than butanol. In some variations anorganism described herein is transformed with a nucleic acid to decreaseor impair expression of a gene product leading to production of asolvent other than ethanol. In some variations an organism describedherein is transformed with a nucleic acid to decrease or impairexpression of a gene product leading to production of a solvent otherthan acetone.

Sugar Transport Genes

As demonstrated in FIG. 5, sugar transporters in thephosphoenolpyruvate-dependent phosphoryltransferase system (PTS) aredown-regulated in BA101 relative to the wild-type strain. BA101 showssignificantly lower expression of mannose-type PTS components ManIIABand ManIIC, which mediate broad spectrum sugar uptake across the cellmembrane.

In some variations, an organism described herein is optimized todecrease production of a gene product relating to one or more specificsugar transporters. In some variations, an organism described herein istransformed with a gene that decreases or knocks out the expression oractivity of a gene product relating to one or more specific sugartransporters.

In some variations, an organism described herein is optimized todecrease production of all of the gene products described hereinrelating to one or more specific sugar transporters. In some variations,an organism described herein is transformed with a gene that decreasesor knocks out the expression or activity of all of the gene productsdescribed herein relating to one or more specific sugar transporters.

In some variations, an organism described herein is optimized todecrease production of ManIIAB. In some variations, an organismdescribed herein is transformed with a nucleic acid to decreaseexpression of a ManIIAB gene. In some variations an organism describedherein is transformed with a nucleic acid to decrease expression of aManIIAB gene via antisense, siRNA, or DNAzyme technology. In somevariations, an organism described herein is transformed with a gene froma microbial organism to decrease expression of ManIIAB. In somevariations, an organism described herein is transformed with a gene froma Clostridium sp. to decrease expression of ManIIAB. In some variations,an organism described herein is transformed with a gene from Clostridiumbeijerinckii to decrease expression of ManIIAB. In some variations, anorganism described herein is transformed with a nucleic acid whichresults in a decrease in expression of the ManIIAB gene whose DNAsequence is shown in FIG. 16.

In some variations, an organism described herein is optimized todecrease production of ManIIC. In some variations, an organism describedherein is transformed with a ManIIC gene. In some variations an organismdescribed herein is transformed with a ManIIC gene to overexpressManIIC.

In some variations, an organism described herein is optimized todecrease production of ManIIC. In some variations, an organism describedherein is transformed with a nucleic acid to decrease expression of aManIIC gene. In some variations an organism described herein istransformed with a nucleic acid to decrease expression of a ManIIC genevia antisense, siRNA, or DNAzyme technology. In some variations, anorganism described herein is transformed with a gene from a microbialorganism to decrease expression of ManIIC. In some variations, anorganism described herein is transformed with a gene from a Clostridiumsp. to decrease expression of ManIIC. In some variations, an organismdescribed herein is transformed with a gene from Clostridiumbeijerinckii to decrease expression of ManIIC. In some variations, anorganism described herein is transformed with a nucleic acid whichresults in a decrease in expression of the ManIIC gene whose DNAsequence is shown in FIG. 17.

Sporulation Genes

Sporulation genes are activated as cells reach stationary phase andenter solventogenic stage. Sporulation is generally believed to benecessary for solvent formation. As demonstrated in FIG. 6, among acascade of sporulation events, BA101 is found defective in late stagesporulation. In contrast to large fold induction in the wild-type,activation is much weaker in BA101 for genes encoding sporulationproteins necessary for the completion of spore formation and sporestability. These proteins include spore coat assembly protein SpoIV,spore cortex synthesis protein SpoVB and spore DNA packaging proteinSspA. Deficiency in sporulation possibly prolongs the clostridial formand thereby allows extended solventogenesis in BA101, which may giverise to enhanced butanol formation.

In some variations, an organism described herein is optimized todecrease production of a gene product relating to sporulation. In somevariations, an organism described herein is transformed with a gene thatdecreases or knocks out the expression or activity of a gene productrelating to sporulation.

In some variations, an organism described herein is optimized todecrease production of all of the gene products described hereinrelating to sporulation. In some variations, an organism describedherein is transformed with a gene that decreases or knocks out theexpression or activity of all of the gene products described hereinrelating to sporulation.

In some variations, an organism described herein is optimized todecrease production of SpoIVA. In some variations, an organism describedherein is transformed with a gene that decreases or knocks out theexpression or activity of SpoIVA. In some variations, an organismdescribed herein is transformed with a nucleic acid to decreaseexpression of a SpoIVA gene. In some variations an organism describedherein is transformed with a nucleic acid to decrease expression of aManIIAB gene via antisense, siRNA, or DNAzyme technology. In somevariations, an organism described herein is transformed with a nucleicacid sequence from a microbial organism to decrease expression ofSpoIVA. In some variations, an organism described herein is transformedwith a gene from a Clostridium sp. to decrease expression of SpoIVA. Insome variations, an organism described herein is transformed with a genefrom Clostridium beijerinckii to decrease expression of SpoIVA. In somevariations, an organism described herein is transformed with a nucleicacid which results in a decrease in expression of the SpoIVA gene whoseDNA sequence is shown in FIG. 18.

In some variations, an organism described herein is optimized todecrease production of SpoVB. In some variations, an organism describedherein is transformed with a gene that decreases or knocks out theexpression or activity of SpoVB. In some variations, an organismdescribed herein is transformed with a nucleic acid to decreaseexpression of a SpoVB gene. In some variations an organism describedherein is transformed with a nucleic acid to decrease expression of aManIIAB gene via antisense, siRNA, or DNAzyme technology. In somevariations, an organism described herein is transformed with a gene froma Clostridium sp. to decrease expression of SpoVB. In some variations,an organism described herein is transformed with a gene from Clostridiumbeijerinckii to decrease expression of SpoVB. In some variations, anorganism described herein is transformed with a nucleic acid whichresults in a decrease in expression of the SpoVB gene whose DNA sequenceis shown in FIG. 19.

In some variations, an organism described herein is optimized todecrease production of SspA. In some variations, an organism describedherein is transformed with a gene that decreases or knocks out theexpression or activity of SspA. In some variations, an organismdescribed herein is transformed with a nucleic acid to decreaseexpression of an SspA gene. In some variations an organism describedherein is transformed with a nucleic acid to decrease expression of anSspA gene via antisense, siRNA, or DNAzyme technology. In somevariations an organism described herein is transformed with an antisensenucleic acid to decrease expression of an SspA gene. In some variations,an organism described herein is transformed with a nucleic acid sequencefrom a microbial organism to decrease expression of SspA. In somevariations, an organism described herein is transformed with a gene froma Clostridium sp. to decrease expression of SspA. In some variations, anorganism described herein is transformed with a gene from Clostridiumbeijerinckii to decrease expression of SspA. In some variations, anorganism described herein is transformed with a nucleic acid whichresults in a decrease in expression of the SspA gene whose DNA sequenceis shown in FIG. 20 (SEQ ID NO: 11). The Clostridium beijerinckii NCIMB8052 published genome identifies this SspA gene as Cbei_(—)3080.

In some variations, an organism described herein is transformed with aSspA gene whose DNA sequence is at least 60-100% identical to the DNAsequence shown in FIG. 20 or complement thereof. In some variations, anorganism described herein is transformed with a SspA gene whose DNAsequence is at least 80-100% identical to the DNA sequence shown in FIG.20 or complement thereof. In some variations, an organism describedherein is transformed with a SspA gene whose DNA sequence is at least90-100% identical to the DNA sequence shown in FIG. 20 or complementthereof. In some variations, an organism described herein is transformedwith a SspA gene whose DNA sequence is at least 60, at least 65, atleast 70, at least 75, at least 80, at least 85, at least 90, at least95, or 100% identical to the DNA sequence shown in FIG. 20 or complementthereof. In some variations, an organism described herein is transformedwith a SspA gene whose DNA sequence is at least 80% identical to the DNAsequence shown in FIG. 20 or complement thereof. In some variations, anorganism described herein is transformed with a SspA gene whose DNAsequence is at least 85% identical to the DNA sequence shown in FIG. 20or complement thereof. In some variations, an organism described hereinis transformed with a SspA gene whose DNA sequence is at least 90%identical to the DNA sequence shown in FIG. 20 or complement thereof.

The C. beijerinckii NCIMB 8052 published genome identifies the SspA geneshown in FIG. 20 as Cbei_(—)3080 (SEQ ID NO:11). It is annotated inGenBank as a “small acid-soluble spore protein, alpha/beta type.”

Other genes identified in the C. beijerinckii NCIMB 8052 publishedgenome that are close homologs of the sspA gene Cbei_(—)3080 (SEQ IDNO:11) include Cbei_(—)3111 and Cbei_(—)3250. They belong to a family ofhighly conserved spore proteins that are present in this organism andare annotated with the same function—“small acid-soluble spore proteinalpha/beta type”—as is Cbei_(—)3080 (SEQ ID NO:11) shown in FIG. 20. Atthe protein sequence level Cbei_(—)3111 is 98% similar and 91% identicalto Cbei_(—)3080. Cbei_(—)3250 is 94% similar and 91% identical.

The utility of Cbei_(—)3111 and Cbei_(—)3250 would be the same as thattaught for Cbei_(—)3080 in the patent, which is to reduce or eliminatetheir expression through a variety of methods.

The DNA sequence of Cbei_(—)3111 (SEQ ID NO: 16) shown in FIG. 23A andthe protein sequence of Cbei_(—)3111 (SEQ ID NO: 17) shown in FIG. 23B.

The DNA sequence of Cbei_(—)3250 (SEQ ID NO: 18) shown in FIG. 24A andthe protein sequence of Cbei_(—)3250 (SEQ ID NO: 19) shown in FIG. 24B.

Chemotaxis Genes

As demonstrated in FIG. 7, BA101 has higher expression of chemotaxis andmotility genes than the wild-type strain. Genes in a chemotaxis operonCheA, CheC, CheD and CheW become repressed in the wild-type during thesolventogenic phase, while their expression levels remain stable inBA101. As highly solventogenic clostridia are generally associated withhigh motility, BA101 appears to remain in a motile form which may befavorable to solvent production.

In some variations, an organism described herein is optimized toincrease production of one or more chemotaxis or motility genes. In somevariations, an organism described herein is transformed with a geneencoding one or more chemotaxis or motility genes. In some variations anorganism described herein is transformed with a gene encoding one ormore chemotaxis or motility genes to overexpress one or more of thechemotaxis or motility genes.

In some variations, an organism described herein is optimized toincrease production of all of the chemotaxis or motility genes describedherein. In some variations, an organism described herein is transformedwith genes encoding all of the chemotaxis or motility genes describedherein. In some variations an organism described herein is transformedwith genes encoding all of the chemotaxis or motility genes describedherein to overexpress all of the chemotaxis or motility genes describedherein.

In some variations, an organism described herein is optimized toincrease production of CheA. In some variations, an organism describedherein is transformed with a CheA gene. In some variations an organismdescribed herein is transformed with a CheA gene to overexpress CheA. Insome variations, an organism described herein is optimized to increaseproduction of CheA in the solventogenic phase. In some variations, anorganism described herein is transformed with a CheA gene. In somevariations an organism described herein is transformed with a CheA geneto overexpress CheA in the solventogenic phase. In some variations, anorganism described herein is transformed with a CheA gene from amicrobial organism to overexpress CheA. In some variations, an organismdescribed herein is transformed with a CheA gene from a Clostridium sp.to overexpress CheA. In some variations, an organism described herein istransformed with a CheA gene from Clostridium beijerinckii tooverexpress CheA. In some variations, an organism described herein istransformed with a nucleic acid which results in an increase inexpression of the CheA gene whose DNA sequence is shown in FIG. 13. Insome variations, an organism described herein is transformed with a CheAgene whose DNA sequence is shown in FIG. 13 to overexpress CheA.

In some variations, an organism described herein is transformed with aCheA gene whose DNA sequence is at least 60-100% identical to the DNAsequence shown in FIG. 13 or complement thereof. In some variations, anorganism described herein is transformed with a CheA gene whose DNAsequence is at least 80-100% identical to the DNA sequence shown in FIG.13 or complement thereof. In some variations, an organism describedherein is transformed with a CheA gene whose DNA sequence is at least90-100% identical to the DNA sequence shown in FIG. 13 or complementthereof. In some variations, an organism described herein is transformedwith a CheA gene whose DNA sequence is at least 60, at least 65, atleast 70, at least 75, at least 80, at least 85, at least 90, at least95, or 100% identical to the DNA sequence shown in FIG. 13 or complementthereof. In some variations, an organism described herein is transformedwith a CheA gene whose DNA sequence is at least 80% identical to the DNAsequence shown in FIG. 13. In some variations, an organism describedherein is transformed with a CheA gene whose DNA sequence is at least85% identical to the DNA sequence shown in FIG. 13 or complementthereof. In some variations, an organism described herein is transformedwith a CheA gene whose DNA sequence is at least 90% identical to the DNAsequence shown in FIG. 13 or complement thereof.

In some variations, an organism described herein is optimized toincrease production of CheC. In some variations, an organism describedherein is transformed with a CheC gene. In some variations an organismdescribed herein is transformed with a CheC gene to overexpress CheC. Insome variations, an organism described herein is optimized to increaseproduction of CheC in the solventogenic phase. In some variations, anorganism described herein is transformed with a CheC gene. In somevariations an organism described herein is transformed with a CheC geneto overexpress CheC in the solventogenic phase. In some variations, anorganism described herein is transformed with a CheC gene from amicrobial organism to overexpress CheC. In some variations, an organismdescribed herein is transformed with a CheC gene from a Clostridium sp.to overexpress CheC. In some variations, an organism described herein istransformed with a CheC gene from Clostridium beijerinckii tooverexpress CheC. In some variations, an organism described herein istransformed with a nucleic acid which results in an increase inexpression of the CheC gene whose DNA sequence is shown in FIG. 14. Insome variations, an organism described herein is transformed with a CheCgene whose DNA sequence is shown in FIG. 14 to overexpress CheC.

In some variations, an organism described herein is transformed with aCheC gene whose DNA sequence is at least 60-100% identical to the DNAsequence shown in FIG. 14 or complement thereof. In some variations, anorganism described herein is transformed with a CheC gene whose DNAsequence is at least 80-100% identical to the DNA sequence shown in FIG.14 or complement thereof. In some variations, an organism describedherein is transformed with a CheC gene whose DNA sequence is at least90-100% identical to the DNA sequence shown in FIG. 14 or complementthereof. In some variations, an organism described herein is transformedwith a CheC gene whose DNA sequence is at least 60, at least 65, atleast 70, at least 75, at least 80, at least 85, at least 90, at least95, or 100% identical to the DNA sequence shown in FIG. 14 or complementthereof. In some variations, an organism described herein is transformedwith a CheC gene whose DNA sequence is at least 80% identical to the DNAsequence shown in FIG. 14 or complement thereof. In some variations, anorganism described herein is transformed with a CheC gene whose DNAsequence is at least 85% identical to the DNA sequence shown in FIG. 14or complement thereof. In some variations, an organism described hereinis transformed with a CheC gene whose DNA sequence is at least 90%identical to the DNA sequence shown in FIG. 14 or complement thereof.

In some variations, an organism described herein is optimized toincrease production of CheD. In some variations, an organism describedherein is transformed with a CheD gene. In some variations an organismdescribed herein is transformed with a CheD gene to overexpress CheD. Insome variations, an organism described herein is optimized to increaseproduction of CheD in the solventogenic phase. In some variations, anorganism described herein is transformed with a CheD gene. In somevariations an organism described herein is transformed with a CheD geneto overexpress CheD in the solventogenic phase.

In some variations, an organism described herein is optimized toincrease production of CheW. In some variations, an organism describedherein is transformed with a CheW gene. In some variations an organismdescribed herein is transformed with a CheW gene to overexpress CheW. Insome variations, an organism described herein is optimized to increaseproduction of CheW in the solventogenic phase. In some variations, anorganism described herein is transformed with a CheW gene. In somevariations an organism described herein is transformed with a CheW geneto overexpress CheW in the solventogenic phase. In some variations, anorganism described herein is transformed with a CheW gene from amicrobial organism to overexpress CheW. In some variations, an organismdescribed herein is transformed with a CheW gene from a Clostridium sp.to overexpress CheW. In some variations, an organism described herein istransformed with a CheW gene from Clostridium beijerinckii tooverexpress CheW. In some variations, an organism described herein istransformed with a nucleic acid which results in an increase inexpression of the CheW gene whose DNA sequence is shown in FIG. 15. Insome variations, an organism described herein is transformed with a CheWgene whose DNA sequence is shown in FIG. 15 to overexpress CheW.

In some variations, an organism described herein is transformed with aCheW gene whose DNA sequence is at least 60-100% identical to the DNAsequence shown in FIG. 15 or complement thereof. In some variations, anorganism described herein is transformed with a CheW gene whose DNAsequence is at least 80-100% identical to the DNA sequence shown in FIG.15 or complement thereof. In some variations, an organism describedherein is transformed with a CheW gene whose DNA sequence is at least90-100% identical to the DNA sequence shown in FIG. 15 or complementthereof. In some variations, an organism described herein is transformedwith a CheW gene whose DNA sequence is at least 60, at least 65, atleast 70, at least 75, at least 80, at least 85, at least 90, at least95, or 100% identical to the DNA sequence shown in FIG. 15 or complementthereof. In some variations, an organism described herein is transformedwith a CheW gene whose DNA sequence is at least 80% identical to the DNAsequence shown in FIG. 15 or complement thereof. In some variations, anorganism described herein is transformed with a CheW gene whose DNAsequence is at least 85% identical to the DNA sequence shown in FIG. 15or complement thereof. In some variations, an organism described hereinis transformed with a CheW gene whose DNA sequence is at least 90%identical to the DNA sequence shown in FIG. 15 or complement thereof.

To develop an organism that can tolerate various inhibitors and productsin the solvent production process, analysis of the mechanism oftolerance may be investigated. In some variations DNA microarrayanalysis is used to study the global or selected expression profiles ofan organism described herein when exposed to various inhibitors orproducts in order to identify the organism's genetic responses. Inaddition, microarray analysis may be used to examine specific enzymes(glycolytic and non-glycolytic) that may be inhibited by thesedegradation compounds. Enzymes of particular interest include alcoholdehydrogenase, phosphofructokinase, glucokinase, galactokinase, aldehydedehydrogenase, pyruvate dehydrogenase complex, butyryl-CoAdehydrogenase, butyrate kinase, etc.

In some variations, an organism described herein is optimized foralcohol dehydrogenase tolerance to inhibitors and products in thesolvent production process. In some variations, an organism describedherein is optimized for butyryl-CoA dehydrogenase tolerance toinhibitors and products in the solvent production process. In somevariations, an organism described herein is optimized for butyratekinase tolerance to inhibitors and products in the solvent productionprocess.

In some variations, an organism described herein is optimized forphosphofructokinase tolerance to inhibitors and products in the solventproduction process. In some variations, an organism described herein isoptimized for glucokinase tolerance to inhibitors and products in thesolvent production process. In some variations, an organism describedherein is optimized for galactokinase tolerance to inhibitors andproducts in the solvent production process. In some variations, anorganism described herein is optimized for aldehyde dehydrogenasetolerance to inhibitors and products in the solvent production process.In some variations, an organism described herein is optimized forpyruvate dehydrogenase complex tolerance to inhibitors and products inthe solvent production process.

Methods of Optimizing Organisms for Use in Industrial Applications

In some variations, an organism described herein is optimized so as tobe more tolerant of industrial conditions. In some variations, anorganism described herein is subjected to a selection process under theindustrial condition of interest, and the most adapted cells areidentified. In some variations, an organism described herein issubjected to mutagenesis, subsequently subjected to a selection processunder the industrial condition of interest, and the most adapted cellsare identified. In some variations an organism described herein istransformed with one or more genes or regulatory sequences givingincreased tolerance or resistance to an industrial condition ofinterest, and the most adapted cells are identified.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more aspects or by-productsof pretreatment. In some variations, an organism described herein isoptimized to increase tolerance or resistance to one or more of salt,acetate, furfural, hydroxymethylfurfural, acetic acid, ferulic acid,glucuronic acid, rhoumaric acid, and phenolic compounds.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to rhoumaric acid. In some variations,an organism described herein is optimized to increase tolerance orresistance to ferulic acid.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to salt.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more intermediates orproducts generated in the solventogenic process.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more specific solventrecovery methods, including but not limited to gas stripping andadsorption or selective membranes.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more temperatures utilized inthe solventogenic process.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more salts encountered in thesolventogenic process.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more pH conditions utilizedin the solventogenic process.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more continuous processingconditions utilized in the solventogenic process.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more solvents generated inthe solventogenic process.

In some variations, an organism described herein is optimized toincrease tolerance or resistance to one or more feedstock materials inthe solventogenic process.

EXAMPLES

Clostridial fermentation cultures were grown for both C. beijerinckiiNCIMB 8052 and the hyper-butanol-producing mutant BA101 ATCC No.PTA-1550. Samples were collected at various time points over the courseof fermentation. Total RNA was isolated from each time point sample.Dye-labeled DNA was generated by reverse transcription from total RNAand used as a sample probe in microarray hybridization. An RNA pool wasconstructed by mixing samples obtained from different stages of cellgrowth. Dye-labeled DNA probe derived from this RNA pool was used as areference probe in microarray hybridization.

The DNA microarray included ˜500 predicted protein-coding genes based onthe draft sequence of C. beijerinckii NCIMB 8052 provided by the JointGenome Institute, available at www.jgi.doe.gov and at GenBank asaccession number CP000721. The array represented 10 functional classescovering ˜10% of the genome.

Example 1 Bacterial Strains and Fermentation Protocols

Bacterial strains and growth conditions. C. beijerinckii NCIMB 8052 isthe wild-type strain. BA101 is the hyper butanol-producing mutantstrain. Stocks of the wild-type and BA101 spores were stored in sterilenanopure H₂O at 4° C.

Fermentation protocols. 1 ml C. beijerinckii spore suspensions were heatshocked at 80° C. for 10 min, and inoculated into 100 mltryptone-glucose-yeast extract (TGY) media containing 3% tryptone, 2%glucose, 1% yeast extract and 0.1% L-cysteine-HCl. The TGY culture wasgrown at 35° C. for 12 hrs in an anaerobic chamber (Coy LaboratoryProducts) maintained under a gas mixture of 85% N2, 10% CO2 and 5% H2.The culture was diluted 10⁶-10⁷ fold into 0.45% liquefied TGY-agar andthe mixture was allowed to solidify in plates in the anaerobic chamber.Plates were incubated at 35° C. for 2-3 days. Individual coloniesdeveloped on the plates were inoculated into 30 ml cooked meat medium(CMM, Oxoid #CM0081) plus added 1% glucose. The CMM culture was grown at35° C. for 9 hrs in the anaerobic chamber. Subsequently, 10 ml CMMculture was inoculated into fresh 100 ml TGY media and grown at 35° C.for 3 hrs in the anaerobic chamber. An aliquot of 20 ml TGY pre-culturewas inoculated into 1.7 liter P2 media containing P2 solutionssupplemented with 6% glucose and 0.1% yeast extract in a fermentationreactor (New Brunswick Scientific). The P2 culture was grown at 35° C.under nitrogen flow. Fermentation samples were taken at various timepoints for analysis.

Example 2 Fermentation Sample Analysis

Aliquots of 1 ml fermentation culture grown in P2 media were collectedat various time points for both C. beijerinckii NCIMB 8052 and BA101.

Cell growth was monitored by measuring the absorbance at 600 nm with aspectrophotometer (Beckman Coulter). Results are depicted in FIG. 1A.The growth curve for the two strains was very similar under theseconditions.

Changes in pH were monitored by sampling the liquid culture using a pHmeter. Results are depicted in FIG. 1B. The pH of the liquid culture wassimilar under these conditions, though the C. beijerinckii NCIMB 8052liquid culture had a higher pH at the later timepoints.

Culture supernatants were analyzed for solvent and acid contents usinggas chromatography (Agilent Technologies). Results are shown in FIG. 2A,FIG. 2B, and FIG. 2C. Total solvents were similar in the two strainsuntil about 20 hours, after which point the level of solvents wasconsistently higher in the BA101 strain.

Example 3 RNA Sampling and Isolation

Aliquots of 10 ml fermentation culture in P2 media were obtained atvarious time points for both C. beijerinckii NCIMB 8052 and BA101. Cellswere pelleted by centrifuging at 4000 g for 10 min. Total RNA wasextracted from the cell pellets using a RNeasy mini kit (Qiagen)according to the manufacturer's protocol. RNA quality was determinedwith nanochip on an Agilent 2100 Bioanalyzer (Agilent Technologies). RNAconcentration was quantified by measuring A260 using a UV/visspectrophotometer (Biotek Instruments). Purified samples were stored inaliquots at −80° C.

To make a reference for comparing gene expression in the time coursesamples, a RNA pool was prepared and used to generate an oppositelylabeled probe in microarray hybridization. To do so, a group of 500 mlstatic flask cultures were grown in P2 media for C. beijerinckii NCIMB8052. The cultures were harvested at different stages of cell growthover the course of fermentation and total RNA was extracted from eachcell pellet. An RNA pool was generated by mixing equal quantities ofpurified RNA from each growth phase, and this mixture was used to createa reference probe for microarray hybridization.

Example 4 Microarray Construction

DNA microarray was constructed by spotting long oligonucleotide probesonto a glass slide (UIUC Functional Genomics Keck Center). A 70-merprobe was selected for a single predicted open reading frame (ORF) inthe sequenced C. beijerinckii genome (Illumina). Each probe was printedin duplicate on the array slide. Each array includes 485 predicted ORFsrepresenting 10 functional classes and approximately 1/10 of the genomebased on the draft sequence assembly of C. beijerinckii NCIMB 8052(Joint Genome Institute). The C. beijerinckii NCIMB 8052 genes includedin the microarray analysis are shown in Table 1, below.

Each gene is associated with a unique gene ID according to the JGIannotation available at the time when the list was compiled formicroarray construction.

TABLE 1 Gene name Gene ID Transcriptional regulator AbrB 1 Probableglucose kinase 11 Spo0A protein (CheY-like receiver domain and HTH-typeDNA binding domain) 54 SpoIVB 55 Exonuclease VII small subunit 62Exonuclease VII large subunit 63 Critical stage III sporulation proteinAH 67 Stage III sporulation protein AG, SpoIIIAG 68 Stage IIIsporulation protein AF, SpoIIIAF, putative 69 Stage III sporulationprotein AE, SpoIIIAE 70 Stage III sporulation protein AD SpoIIIAD 71Stage III sporulation protein AC, SpoIIIAC 72 Stage III sporulationprotein AB, SpoIIIAB 73 Stage III sporulation protein AA, SpoIIIAA 74CDP-diglyceride synthetase 90 Pseudouridine synthase 102 Riboflavinkinase/FAD synthase 103 Ribosomal Protein S15 104 Periplasmic serineprotease, YMFB B. subtilis ortholog 109 Speculation protein SpoIIIE, DNAsegregation ATPase 110 Predicted Fe—S oxidoreductase 111 Catabolicacetolactate synthase 139 Aspartyl/asparaginyl-tRNA synthetase 168Ribose 5-phosphate isomerase A 175 Putative alternative nitrogenasemolybdenum-iron protein, NifD- or NifE-like 193 Putative alternativeFeMo-cofactor synthesis protein, NifB-like 196 Putative alternativenitrogenase iron protein, NifH-like 201 Putative alternative nitrogenasemolybdenum-iron protein, NifD- or NifE-like 204 Stage V sporulationprotein 217 Asparagine synthase, N-terminal domain 218 ABC-typemulti-drug/protein/lipid transport system, membrane ATPase component 225NH₃-dependent NAD synthase fused to amidohydrolase domain 228 DSBHdomain-containing protein 229 RecG helicase 235 Phosphopantetheineadenylyltransferase 237 Phosphotransacetylase 241 Acetate kinase 242Acyl carrier protein ACP 246 ADP-glucose pyrophosphorylase 253ADP-glucose pyrophosphorylase 254 Glycogen phosphorylase 256 Glycogensynthase, GlgA 257 L-lactate dehydrogenase 290 Acyl-coA dehydrogenase:butyryl-CoA dehydrogenase 292 Formate acetyltransferase 293Pyruvate-formate lyase 295 6-Phosphofructokinase 306 RecA recombinase,ATPase 310 Stage V sporulation protein S, SpoVS 312 Beta-galactosidase324 Beta-galactosidase 328 DNA-dependent RNA polymerase sigma subunit345 Specialized DNA-dependent RNA polymerase sigma subunit 346 Responseregulator (CheY-like receiver domain and HTH-type DNA-binding domain)350 Permease component of ATP-dependent phosphate uptake system 354 Fe—Soxidoreductase, related to NifB/MoaA family with PDZ N-terminal domain358 Glycerol 3-phosphate dehydrogenase 360 Coat morphogenesissporulation protein SpoIVA 361 Uncharacterized stress-induced protein,YicC family 364 RNA polymerase-associated protein RpoZ, omega subunit,YLOH B. subtilis ortholog 367 Flavoprotein involved in panthothenatemetabolism, YLOI B. subtilis ortholog 368 Primosomal protein N′,superfamily II helicase 369 Ribulose-phosphate 3-epimerase 378 Ribosomalprotein L28 380 Ribosomal protein L2 410 Adenylate kinase 428DNA-dependent RNA polymerase alpha subunit 436 ABC-type transporter,ATPase component, cobalt transporters subfamily 439 Probable sporecortex lytic enzyme 455 Phosphotransbutyrylase, Ptb 459 Butyrate kinase,Buk 460 Flagellar motor switch protein, FliG 471 Ethanolamineutilization protein, EutE 499 Ribose 5-phosphate isomerase A 537Alpha-L-arabinofuranosidase 544 Putative pyruvate kinase 555 Criticalsmall acid-soluble spore protein, alpha/beta type 559 ATPases withchaperone activity ClpC, two ATP-binding domains 587 RNAmethyltransferase Trmlt family, group 3 597 Acyl-coA dehydrogenase:butyryl-CoA dehydrogenase 617 Critical probable spore coat protein 650Putative spore coat protein 651 Spore coat protein S 652 Mannosyltransferase 653 Probable spore coat protein 654 Stage II sporulationprotein 662 DNA gyrase (topoisomerase II) subunit A 671 DNA gyrase(topoisomerase II) subunit B 672 RecF, ABC family ATPase 674 DNApolymerase III beta subunit 676 DNA replication initiator protein,ATPase 677 Stage III sporulation protein J, SpoIII J 681 SpoIIIJ-associated protein 682 Stage O sporulation protein J, SpoOJ 686 Spo0Aactivation inhibitor 687 Stage O sporulation protein J, SpoOJ 688 Singlestrand DNA-binding protein Ssb 697 Uncharacterized conserved protein,CotF B. subtilis ortholog 718 VWA domain-containing CoxE-like proteinfamily 731 Membrane permease, predicted cation efflux pumps 741Predicted Co/Zn/Cd cation transporter 759 Regulatory protein TenI 775Uncharacterized protein containing two CBS domains 779 Transcriptionalregulator, LysR family 793 Phosphoglycerate mutase family protein 8263-Oxoacyl-(acyl carrier protein) reductase 834 Alcohol dehydrogenase 873Possible phosphoglycerate mutase 875 Uncharacterized oxidoreductase,Fe-dependent alcohol dehydrogenase family 902 Fructose-bisphosphatealdolase 930 Probable tagatose-6-phosphate kinase, AgaZ 972 Probabletagatose-6-phosphate kinase 973 Small acid-soluble spore protein beta1029 Small acid-soluble spore protein 1030 Fructose-1,6-bisphosphatase,YYDE B. subtils ortholog 1033 Cytosine deaminase 1074 Cyclopropane fattyacid synthase 1079 ABC-type probable sulfate transporter, periplasmicbinding protein 1097 Bifunctional enzymephosphoribosyl-formyl-glycinamidine (FGAM) synthase 12233-Oxoacyl-[acyl-carrier-protein] synthase III 1238 Dioxygenase 1239Malonyl CoA-acyl carrier protein transacylase 12403-Oxoacyl-[acyl-carrier-protein] reductase 12413-Oxoacyl-[acyl-carrier-protein] synthase II 1242 Acetyl-CoA carboxylase1243 FabZ 1244 Acetyl-CoA carboxylase: biotin carboxylase 1245Acetyl-CoA carboxylase subunit beta 1246 Acetyl-CoA carboxylase carboxyltransferase subunit alpha 1247 Predicted endonuclease involved inrecombination 1274 Ferric uptake regulation protein 1276 DNA-dependentRNA polymerase sigma subunit 1283 Cell division GTPase FtsZ 1286Recombination protein RecR 1313 DNA-directed DNA polymerase III chain,DnaX 1315 Pyruvate carboxylase 1324 Xylan 1,4-beta-xylosidase 1336 Sigmafactor SigK processing regulatory protein, BofA B. subtilis ortholog1359 Phosphoenolpyruvate synthase 1376 Pyruvate water dikinase 1379Spore coat protein CotJC 1382 Histidine kinase 1385 Long-chain fattyacid-CoA ligase 1407 4-Hydroxybutyryl-CoA dehydratase 1411 Arsenatereductase, ArsC, tyrosine-phosphatase family enzyme 1422 Spore coatpeptide assembly protein CotJB 1434 Transketolase 1450 BifunctionalD-arabino 3-hexulose-6-phosphate formaldehyde 1453lyase/phosphohexuloisomerase Beta-glucosidase 1475 ABC transporter,ATP-binding component 1477 Xylose isomerase 1504 xylulose kinase 1505Transaldolase, putative 1507 3-Oxoacyl-[acyl-carrier-protein] reductase1519 Activator of 2-hydroxyglutaryl-CoA dehydratase 1526 NADH-dependentbutanol dehydrogenase BDH II 1542 MDR-type permease 1577 Responseregulator (CheY-like receiver domain and DNA-binding HTH domain) 1599Regulator of stationary/sporulation gene expression AbrB-like gene 1615Phosphoglycerate mutase 1662 Critical small acid-soluble spore protein,alpha/beta type 1685 Small acid-soluble spore protein SspA 1699 SleC1704 Stage V sporulation protein T, transcriptional regulator AbrBhomolog 1745 Ribose 5-phosphate isomerase B 1773 Thiolase, acetyl-CoAacetyltransferase 1777 Stage III sporulation protein D, spore proteaseGpr-related protein 1788 Hypothetical protein 1790 Spore proteaseGpr-related protein, YYAC B. subtilis ortholog 1792 Predictediron-binding protein, hemerythrin 1829 Critical small acid-soluble sporeprotein 1840 Pyruvate kinase 1851 Alcohol dehydrogenase, zinc-dependent1873 Transketolase, N-terminal section 1874 Transketolase, C-terminalsection 1875 Ribulose-phosphate 3-epimerase 1876 Ribose 5-phosphateisomerase B 1877 ABC-type transport system, ATPase component 1887Long-chain fatty acid-CoA ligase 1903 Malonyl CoA-acyl carrier proteintransacylase 1906 Small acid-soluble spore protein beta 1927Histidinol-phosphate aminotransferase 1941 1-Phosphofructokinase 1972Pyruvate ferredoxin oxidoreductase 1982 Predicted oxidoreductase, GSP39B. subtilis ortholog 1988 Uncharacterized protein, YPUG B. subtilisortholog 2004 Putative 4-cys ferredoxin 2009 SpoU 2018 PredictedS-adenosylmethionine-dependent methyltransferase 2022 Stage Vsporulation protein D, SpoVD, FtsI/pbp family 2024 Stage V sporulationprotein D, SpoVD, FtsI/pbp family 2025 Stage V sporulation protein E,SpoVE 2029 Chemotaxis motility protein B, MotB 2038 Chemotaxis motilityprotein A, MotA 2039 Butyryl-CoA dehydrogenase 2135 Homocitrate synthasesubunit alpha, NifV 2156 Putative NirJ1 protein 2161 Putative [2Fe—2S]ferredoxin, FdxA 2162 FeMo-cofactor synthesis protein, NifN 2163 FeMocofactor synthesis protein, NifE 2164 Nitrogenase molybdenum-ironprotein beta subunit, NifK 2165 Nitrogenase molybdenum-iron proteinalpha subunit, NifD 2166 GlnB-like protein-1 2168 Nitrogenase ironprotein, NifH 2169 Sporulation factor SpoIIM 2206 3-Oxoacyl-(acylcarrier protein) reductase 2207 Aldehyde dehydrogenase; alcoholdehydrogenase 2247 FAD/FMN-containing dehydrogenase 2254 Pyruvateformate-lyase 2257 Pyruvate formate-lyase activating enzyme 22588-Oxoguanine-DNA glycosylases 2268 Co-chaperonin GroES, Hsp10 family2270 Chaperonin GroEL, Hsp60 family 2271 Glucose-6-phosphate isomerase2283 3-Oxoacyl-[acyl-carrier protein] reductase 2303 Streptogramin Blactonase 2386 Hypothetical cytosolic protein 2399 Acetyl-CoAacetyltransferase, thiolase 2402 MDR-type permease, probablytetracycline-resistance protein 2412 Malic enzyme 2425 Predictedaldo/keto reductase, YTBE/YVGN B. subtilis ortholog 2496Phosphoenolpyruvate synthase 2500 Glucose kinase 2501Membrane-associated methyl-accepting chemotaxis protein with HAMP domain2547 Chemotaxis protein CheW 2548 Chemotaxis protein methyltransferase,CheR 2553 Chemotaxis protein CheA 2555 Flagellar motor protein MotB 2556Flagellar motor component MotA 2557 Beta-glucosidase 2559 Pyruvatekinase 2577 Enolase 2578 2,3-Biphosphoglycerate-independentphosphoglycerate mutase gene 2579 Transketolase, C-terminal section 2596Transketolase, N-terminal section 2597 tRNA-processing ribonuclease 2605Protein containing Zn-finger domain 2624 SOS regulatory protein LexA2626 DNA mismatch repair enzyme, MutL 2630 Mismatch repair protein MutS,ATPase 2634 Ketopantoate hydroxymethyltransferase 2674Alpha-galactosidases/6-phospho-beta-glucosidase, family 4 glycosylhydrolase 2726 Stage II sporulation protein 2738 Stage V sporulationprotein B 2745 Stage V sprulation protein T, SpoVT 2746 Stage Vsporulation protein 2754 HD-GYP hydrolase domain-containing protein 2760Spore maturation protein 2782 Pyruvate carboxylase PYKA 2785 Pyruvateformate lyase-activating enzyme 2795 HD-GYP hydrolase domain-containingprotein 2801 Short-chain dehydrogenase: 3-oxoacyl-[acyl-carrier protein]reductase 2805 Transcriptional regulator TetR/AcrR family 2813Phosphatidylserine decarboxylase 2814 Mannose/fructose-specificphosphotransferase system component IIC 2839 Mannose-specificphosphotransferase system component IIAB 2840 Pyruvate formate-lyase2846 Pyruvate formate-lyase activating enzyme 2850 Acyl-acyl carrierprotein thioesterase 2861 Putative acyl-CoA ligase 2868 Aldehydedehydrogenase, NAD-dependent dehydrogenase family 2878 Zinc-containingalcohol dehydrogenase, long-chain 2891 Putative transcription activator,Stc-like 2892 Cation transport P-type ATPase 2906 Septumsite-determining protein, MinD 2941 Stage V sporulation protein E 2943Putative stage IV sporulation protein FB 2945 Biotin carboxylase:acetyl-CoA carboxylase, putative 2948 Protein of unknown functionLDUF464 superfamily 2955 Putative kinase 2970 Ribulose-phosphate3-epimerase 2973 Alcohol dehydrogenase, zinc-dependent 2988Transketolase, N-terminal section 2989 Transketolase, C-terminal section2990 Ribulose-phosphate 3-epimerase 2991 Ribose 5-phosphate isomerase B2992 Ribulose-phosphate 3-epimerase family protein 2995 Similar toribulose-5-phosphate 3-epimerase 2996 Stage V sporulation protein R,SpoVR 3012 6-Phosphofructokinase 3028 VanW-like protein family 3037Glyceraldehyde 3-phosphate dehydrogenase 3041 Phosphoglycerate kinase3042 Triosephosphate isomerase 3043 2,3-Bisphosphoglycerate-independentphosphoglycerate mutase 3044 Phosphopyruvate hydratase 3046 ABC-typesulfate transporter, ATPase component 3054 Putative alternativenitrogenase molybdenum-iron protein, NifD- or NifE-like 3056 ABC-typeprobable sulfate transporter, permease protein 3059 Pyruvate formatelyase-activating enzyme 3069 Pyruvate formate lyase-activating enzyme3070 Ferredoxin 3075 Critical peptidase S16, ATP-dependent protease 3077HD-GYP hydrolase domain-containing protein 3100 Muconatecycloisomerase-related protein, YKGB B. subtilis ortholog 3102Glutamyl-tRNA reductase 3107 Hydroxymethylbilane syntase(porphobilinogen deaminase) 3109 Uroporphyrinogen III syntase 3110Delta-aminolevulinic acid dehydratase (porphobilinogen synthase) 3111Glutamate-1-semialdehyde aminotransferase 3112 Possible cysteinedesulphurase from NifS family 3135 FKBP-type peptidyl-prolylcis-transisomerase (trigger factor) 3149 Critical ClpX, ATPaseregulatory subunit 3151 ATP-dependent Lon protease 3153 Spore cortexprotein 3209 Sporulation protein B 3210 Membrane-associated sensorytransduction histidine kinase (with HAMP domain) 3255 Response regulator(CheY-like receiver domain and HTH DNA-binding domain) 3256 Hydrogenaseexpression/formation protein HypE 3277 Fructose-bisphosphate aldolaseclass I 3310 Beta-xylosidase 3318 Small acid-soluble spore protein SspA3349 Small acid-soluble spore protein, alpha/beta type 3380 Stage Osporulation protein J, putative 3416 Putative transcription activatorStc 3418 Alcohol dehydrogenase 3419 Putative electron-transfer proteinHydG 3420 Alcohol dehydrogenase, iron-containing 3432 Critical smallacid-soluble spore protein, alpha/beta type 3461 Probable enoyl-CoAhydratase 3466 Probable enoyl-CoA hydratase 3467 Alcohol dehydrogenase,zinc-containing 3477 Possible stage V sporulation protein, SpoVT 3499Acyl-CoA dehydrogenase, short-chain specific: butyryl-CoA dehydrogenase3508 Transaldolase 3637 Acetyl-CoA carboxylase (biotin carboxylasesubunit) 3649 Acetyl-CoA carboxylase biotin carboxyl carrier protein3650 L-lactate dehydrogenase 3682 Phosphoglycerate mutase 3691Uncharacterized conserved protein YHAD family 3755 L-lactatedehydrogenase 3774 L-serine dehydratase, iron-sulfur-dependent, betasubunit 3775 Beta-glucosidase 3801 Transcriptional regulator ofNagC/XylR (ROK) family, sugar kinase 3813 Fructose bisphosphatase 3818Propionate-CoA transferase 3820 Crotonase 3821 Fructose-1,6-bisphosphatealdolase 3828 Phosphoglucomutase 3831 Accessory regulator protein B 3855Histidine kinase-like ATPase 3856 Accessory regulatory protein A 3857Flagellar biosynthesis related protein 3885 Spore coat protein, putative3889 Critical spore coat protein, CotF-related 3890 Spore coat protein,putative 3891 Critical spore coat protein, CotF-related 3892(R)-2-hydroxyglutaryl-CoA dehydratase activator-related protein 3926Glucose kinase 3978 3-Hydroxybutyryl-CoA dehydrogenase 3988 ABCtransporter, ATP-binding protein 3993 Aid CoA-acylating aldehydedehydrogenase 3999 Butyrate-acetoacetate CoA-transferase subunit A 4000Butyrate-acetoacetate CoA-transferase subunit B 4001 Acetoacetatedecarboxylase 4002 ABC-type transport system, ATPase component 4022Phosphoenolpyruvate synthase/pyruvate phosphate dikinase 4025 Pyruvatewater dikinase 4028 Zinc-binding dehydrogenase: alcohol dehydrogenase4030 Histidine kinase-like ATPase 4032 Response regulator (CheY-likereceiver domain and HTH DNA-binding domain) 4033 Short-chaindehydrogenase: 3-oxoacyl-[acyl-carrier protein] reductase 4069Nitroreductase family protein 4070 Phosphoglycerate mutase 4085Chemotaxis protein CheW 4116 Alpha-glucosidase 4142 Thioredoxinreductase 4148 Malic enzyme 4150 Anaerobic sulfite reductase subunit B4154 Anti-anti SigF 4182 Anti-sigma factor F, Stage II sporulationprotein AB 4183 Sporulation-specific sigma factor F 4184 Critical SpoVAprotein 4185 IMP dehydrogenase/GMP reductase: Stage V sporulationprotein AD 4186 Stage V sporulation protein AE, SpoVAE 4187 Sporeprotease Gpr 4192 Stage II sporulation protein P, SpoIIP 4193Transcriptional regulator of heat shock genes, Hrc A 4198 Molecularchaperone DnaK, Hsp70 family 4200 Molecular chaperones DnaJ, Hsp40family 4201 Ferredoxin-nitrite reductase 4202 Stage IV sporulationprotein 4211 Spore coat protein S 4220 Predicted dehydrogenase ofshort-chain alcohol dehydrogenase family 4238 TPR repeats-containingprotein 4350 Alpha-galactosidase 4383 Alpha-galactosidase 4384 Thiaminebiosynthesis enzyme ThiH 4386 Spore photoproduct lyase SpIB 4463Melibiase (alpha-galactosidase) 4465 Cysteinesynthase/cystathionine-beta synthase, CysK 4468 DNA gyrase subunit B4500 DNA gyrase subunit A 4501 SsDNA exonuclease RecJ 4503 Pyruvate:ferredoxin oxidoreductase 4506 Chemotaxis protein CheW 4513 Chemotaxisprotein CheD 4514 Chemotaxis protein CheB, containing CheY-like receiverdomain and HTH DNA- 4515 binding domain Chemotaxis proteinmethyltransferase CheR 4516 Chemotaxis histidine kinase CheA, containingCheW-like adaptor domain 4517 Chemotaxis protein CheC 4518 Chemotaxissignal transduction protein CheW 4520 Flagellar switch protein FliM 4521Flagellar switch protein FliY, containing CheC-like domain 4522Flagellar hook-associated protein FlgK 4526 Flagellar hook-associatedprotein 3 4527 Carbon storage regulator 4529 Flagellar protein FliS 4532Flagellar cap protein FliD, putative 4533 Possible hook-associatedprotein, flagellin family 4535 Spore coat polysaccharide biosynthesisprotein 4543 FlaG 4544 Chemotaxis motility protein A, MotA 4551Chemotaxis motility protein B, MotB 4552 Flagellar basal body rodprotein FlgB 4553 Flagellar basal body rod protein FlgC 4554 Flagellarassembly protein FliH, putative 4558 Flagellar-type ATPase 4559Flagellar export protein FliJ 4560 Flagellar hook assembly protein FlgD,putative 4562 Flagellar hook protein flgE 4564 Flagellar protein FlbD4565 Flagellar basal body-associated protein FliL 4566 Flagellarbiosynthesis protein FliP 4568 Flagellar biosynthesis protein FliQ 4569Flagellar biosynthesis protein FlhA 4571 Flagellar GTP-binding proteinFlhF 4572 Sigma factor of SigD/WhiG family 4575 Flagellar basal body rodprotein 4578 General secretion pathway protein, pilin family 4608Ferredoxin 4635 Sulfate adenylate transferase, CysD subfamily 4636GTPase, sulfate adenylate transferase subunit 4637 HD-GYPdomain-containing-protein 4638 Chemotaxis protein CheW 4639 Chemotaxisprotein methyltransferase CheR 4642 Chemotaxis protein/ glutamatemethylesterase 4643 CheY-like receiver domains, putative 4649 ABCtransporter, ATP-binding protein 4656 Hsp 90 4663 Uncharacterizedconserved protein 4670 ATP-dependent Clp proteinase 4671Deoxyribose-phosphate aldolase 4679 HD-GYP hydrolase domain-containingprotein 4683 Beta-xylosidase, family 43 glycosyl hydrolase 4696 Hsp 184699 Glycerol dehydrogenase 4730 L-lactate dehydrogenase 4749 Pyruvateformate-lyase 4760 Glycerol dehydratase activator 4761 Critical IMPdehydrogenase/GMP reductase 4775 Alcohol dehydrogenase/ acetaldehydedehydrogenase 4776 2-Oxoacid: ferredoxin oxidoreductase, alpha subunit4779 3-oxoacyl-[acyl-carrier-protein] synthase III 4789 Activator of2-hydroxyglutaryl-CoA dehydratase 4794 Predicted permease 4797Chemotaxis protein CheY homolog 4801 Chemotaxis protein cheA 4802Chemotaxis protein Chew 4803 Transcriptional regulator, Lrp family 4811Critical endopeptidase Clp 4819 3-Oxoacyl-[acyl-carrier protein]synthase 4831 Lactate dehydrogenase 4866 Small acid-soluble sporeprotein SspC2 4927 L-lactate dehydrogenase 4951 Phosphoglycerate mutase4961 Alpha-xylosidase 4968 Aldehyde dehydrogenase (NAD+) 4974 Criticalbacterial regulatory protein MarR 4976 Topoisomerase I 4983 Acetyl-CoA:acetoacetyl-CoA transferase alpha subunit 4992 Pyruvate kinase, barreldomain 5003 Critical heat shock protein DnaJ, N-terminal domain 5005Butyryl-CoA dehydrogenase, putative 5011 Oligopeptide transport permeaseprotein 5044

Microarray DNA probe labeling and hybridization. Two-color microarrayhybridization was performed using the aminoallyl labeling procedureadapted from a TIGR protocol (UIUC Functional Genomics Keck Center).Briefly, 3 μg of purified total RNA were primed with random hexamers(Pharmacia) and used as templates for DNA synthesis using aminoallyldNTPs (Ambion) and Superscript III reverse transcriptase (Invitrogen) ineach labeling reaction. The aminoallyl-labeled DNAs were coupled to Cy3or Cy5 dye esters (Molecular Probes), and oppositely dye-labeled probeswere hybridized on an array simultaneously. To compare gene expressionin the time course of fermentation, one of the dye-labeled probes wasgenerated from samples collected at individual time points, whereas theother dye-labeled control probe was derived from the RNA pool asdescribed above.

Microarray hybridization was performed using one array for each samplecollected in the fermentation time course. Briefly, the slides wererehydrated, UV cross-linked, and pre-hybridized in 5×SSC, 0.1% (w/v) SDSand 1% (w/v) BSA at 42° C. for 45 min. The slides were then hybridizedwith a mixture of oppositely labeled DNA probes in hybridization buffer(Ambion) at 42° C. for 16-48 hrs. After hybridization, the slides werewashed with 1×SSC and 0.2% (w/v) SDS at 42° C. for 5 min, followed by asecond wash in 0.1×SSC and 0.2% (w/v) SDS at room temperature for 5 min,and a last wash in 0.1×SSC for 5 min. The slides were dried andimmediately scanned on an Axon 4000B scanner (UIUC Functional GenomicsKeck Center). Features in each array were extracted using GenePix Pro6.0.

Results are depicted in FIG. 3A and FIG. 3B for C. beijerinckii NCIMB8052 and BA101, respectively. Expression level is indicated by intensityof the color bar (green to red) based on log₂ transformation of thenormalized expression ratio determined for each gene at individual timepoint. Temporal expression patterns are visualized with hierarchicalclustering for the transition of fermentation cultures from acidogenesisto solventogenesis

Microarray data analysis. Data generated from microarray experimentswere processed and visualized using the TM4 suite (TIGR). Briefly, theexpression ratio (Cy5/Cy3) for a gene in each sample was determinedbased on quantification of the fluorescence intensity for each spot onthe array using GenePix Pro 6.0. The expression ratios obtained from allthe genes on each array were normalized using Midas (TIGR). LOWESSintensity-based normalization was applied in most cases. Normalizedexpression ratios for a gene obtained at the analyzed time points wereused to construct the temporal profiles of gene expression over thecourse of fermentation for C. beijerinckii NCIMB 8052 and BA101,respectively. Global expression patterns were analyzed by averagelinkage hierarchical clustering with Euclidean distance matrices andvisualized colorimetrically using TMEV (TIGR).

Results for mRNA accumulation levels of various enzymes in theClostridial solventogenic pathway were quantitatively depicted in FIG.4. Differential mRNA accumulation of solventogenic genes was compared inC. beijerinckii NCIMB 8052 (♦) versus BA101 (o). Increased expression inBA101 during the solventogenic stage was observed for alcoholdehydrogenase (Adh), butyryl-CoA dehydrogenase (Bcd) and butyrate kinase(Buk).

Results for mRNA accumulation levels of various sugar transporters werequantitatively depicted in FIG. 5. Differential mRNA accumulation ofsugar transporters was compared in C. beijerinckii NCIMB 8052 (♦) andBA101 (o). Components of mannose-family phosphoenolpyruvate(PEP)-dependent phosphotransferase system IIA, IIB (ManIIAB) and IIC(ManIIC) were significantly down-regulated in BA101.

Results for mRNA accumulation levels of various sporulation genes werequantitatively depicted in FIG. 6. Differential expression ofsporulation genes was compared in C. beijerinckii NCIMB 8052 (♦) andBA101 (o). Induction of late stage sporulation factors was much weakerin BA101 than in the wild-type strain. Lowered activation in BA101through the solventogenic phase was observed for coat morphosissporulation protein (SpoIVA), Stage V sporulation protein B (SpoVB) andsmall acid-soluble spore protein (SspA).

Results for mRNA accumulation levels of various chemotaxis genes werequantitatively depicted in FIG. 7. Differential expression of chemotaxisgenes was compared in C. beijerinckii NCIMB 8052 (♦) and BA101 (o).Higher expression levels of CheA, CheC, CheD and CheW in a chemotaxisgene cluster were observed for BA101 during the solventogenic stage.

Results for mRNA accumulation levels of various solventogenic genes werequantitatively depicted in FIG. 8. Solventogenic genes with comparableexpression kinetics were compared in C. beijerinckii NCIMB 8052 (♦) andBA101 (o). Expression of aceto-acetyl CoA:acetate-butyrate CoAtransferase subunit α/β (CtfA/B) and acetoacetate decarboxylase (Adc)was highly activated at the onset of solventogenic phase in BA101 andthe wild-type strain. Changes in expression levels were much smaller forthiolase (Thl), 3-hydroxybutyryl-CoA dehydrogenase (Hcd) and crotonase(Crt) in BA101 and the wild-type strain.

Tables 2A and 2B show subsets of genes that were found to bedifferentially expressed between C. beijerinckii NCIMB 8052 and BA101.

TABLE 2 (A) Genes with increased expression in BA101 compared with thewild-type strain. Functional class Gene name Gene product activitySolventogenesis Alcohol dehydrogenase Catalyzing the reduction ofaldehyde to alcohol Butyryl-CoA dehydrogenase Catalyzing the reductionof crotonyl-CoA to butyryl-CoA Butyrate kinase Catalyzing the generationof butyrate from butyrylphosphate with concurrent ATP synthesisChemotaxis CheA Chemotaxis sensory transducer, histidine kinase CheCChemotaxis protein CheD Chemotaxis methylation system protein CheWChemotaxis protein, histidine kinase

TABLE 2 (B) Genes with reduced expression in BA101 relative to thewild-type strain. Functional class Gene name Gene product activitySporulation Coat morphosis sporulation protein SpoIVA Spore coatassembly Stage V sporulation protein B SpoVB Spore cortex biosynthesisSmall acid-soluble spore protein SspA Packaging and protection of sporeDNA Sugar Mannose-specific phosphoenolpyruvate- Mediating phosphorylrelay for transporters dependent phosphotransferase system themodification of incoming component IIAB sugar Mannose/fructose-specificMediating sugar transport across phosphoenolpyruvate-dependent themembrane through permease phosphotransferase system component IIC

Example 5 General Methods Used in the Examples

PCR primers are designed using the PrimerSelect features of the DNASTARsuite of molecular biology programs from DNAStar, Inc. (Madison, Wis.).Techniques of primer design are known in the art (PCR Primer Design,2007, Anton Yuryev editor, Humana Press).

PCR products are amplified using Takara Ex Taq™ DNA Polymerase fromTakara Bio USA (Madison, Wis.), and a Gene Amp® PCR system 9700thermocycler from Applied Biosystems (Foster City, Calif.). Other DNApolymerase products for PCR provide suitable alternatives. Cyclingparameters can vary according to the specific primers and DNA sequencesbeing amplified. In general the methods and parameters are known in theart. (PCR Protocols, 2nd edition, 2003, John M. S. Bartlett and DavidStirling editors, Humana Press; PCR: The Basics, 2nd edition, 2006, M.J. McPherson and S. G. Moller, Taylor & Francis publisher).

For colony PCR, fresh colonies are picked from Petri plates andsuspended in a 50-100 μL of ultrapure water or 10 mM Tris, pH 7.5. 1-5μL of the cell suspension is substituted for the purified DNA in anormal PCR reaction mixture. The initial PCR heat cycle of the processmay be extended in some cases, for example 10 min at 94° C., to aid incell lysis.

The isolation and purification of plasmid DNA, chromosomal DNA, DNAfragments from preparative agarose gels and PCR products is accomplishedusing commercial kits that are available from various suppliers.Examples of two such suppliers are Qiagen Inc. (Valencia, Calif.) and MOBIO Laboratories (Carlsbad, Calif.). Examples of Qiagen kits for someapplications are “QIAprepe” for plasmid DNA, “QIAquick®” for purifyingDNA fragments from agarose gels, and “QIAquick®” or “MinElute®” forpurifying PCR products. Chromosomal DNA preparations (genomic DNA) areprepared using the “UltraClean Soil DNA Isolation” kit from MO BIOLaboratories.

For introduction of DNA into Clostridium hosts by electroporation(transformation), a culture of the Clostridium strain is grown to anOD₆₀₀ of 0.8, then washed for two cycles with 15% polyethylene glycol(PEG). Electroporation is done in the presence of 10 μg of plasmid DNAusing a cuvette with a 2 mm path in a Bio-Rad Gene Pulser™ exponentialdecay generator set (BioRad, Richmond, Calif.) for 2.0 kV (10 kV/cm),200 ohms and 4.5 ms. Electroporation parameters may vary from strain tostrain. Those skilled in the art will be capable of adjusting parametersas needed (Molecular Cloning: A laboratory manual, 3rd edition, 2001,Joseph Sambrook and David W. Russell, Cold Spring Harbor LaboratoryPress; Handbook on Clostridia, 2005, Peter Durre editor, Taylor &Francis publisher).

General cloning methods such as use of restriction endonucleases, DNAligase and other nucleic acid modification techniques, separativetechniques such as agarose or polyacrylamide gel electrophoresis, andthe like are known in the art and comprehensive guides are available(Methods for General and Molecular Microbiology, 3rd edition, 2007, C.A. Reddy editor in chief, ASM Press; Molecular Genetics of Bacteria, 2ndedition, 2003, Larry Snyder and Wendy Champness, ASM Press; MolecularCloning: A laboratory manual, 3rd edition, 2001, Joseph Sambrook andDavid W. Russell, Cold Spring Harbor Laboratory Press).

Example 6 Construction of Strains of Solventogenic Clostridia whereinspoIVA Gene Expression is Deficient

A mutant derivative of Clostridium beijerinckii strain NCIMB 8052 isconstructed wherein the function of the spoIVA gene encoded by SEQ IDNO: 9 (locus_tag Cbei_(—)1136 of GenBank CP000721) is destroyed byinsertion of a plasmid bearing a cloned fragment of the spoIVA gene DNAinto the chromosome, so as to disrupt the coding sequence of the gene.Insertion of the plasmid into the chromosome takes place bysingle-cross-over homologous recombination between the chromosomalspoIVA gene and the cloned spoIVA fragment.

A spore suspension of Clostridium beijerinckii strain NCIMB 8052 is heatshocked for 10 minutes at 80° C., placed on ice briefly, moved into aCoy® anerobic chamber (Coy Laboratory Products, Grass Lake, Mich.)containing an atmosphere of 85% N₂, 10% CO₂ and 5% H₂, and then used toinoculate 10 mL of TGY medium in an 18 mm diameter test tube. Theculture is grown at 35° C. to an OD₆₀₀ of about 0.6 to 0.8. A 1.0 mLportion of this culture is used to inoculate another 10 mL of TGY, whichis grown to about 0.6 OD₆₀₀, or to a density that yields goodchromosomal DNA preparations. The culture is then harvested andprocessed to prepare purified chromosomal DNA using the “UltraClean™Soil DNA Isolation” kit and protocols from MO BIO Laboratories.

PCR primers incorporating terminal XmaI restriction endonuclease sitesare designed using the PrimerSelect™ software package of DNASTAR Inc.(Madison, Wis.) so as to amplify an internal fragment of the spoIVA geneof preferably 250-600 bp in length, ideally in the central part of thecoding region of the gene; for example, the 3′ one-third of the genepreferably is avoided to prevent partially functioning spoIVA geneproduct in the resulting mutants.

The chosen internal fragment of the spoIVA gene is amplified by the PCRreaction using the purified chromosomal DNA preparation and the chosenPCR primers. The amplified spoIVA internal fragment with the terminalXmaI sites is purified from the finished PCR mixture using QiagenMinElute® spin columns or a similar product. Alternatively the fragmentcould be separated using a preparative agarose gel and purified from agel slice using Qiagen Qiaquick® kits. The purified spoIVA fragment isrestriction digested with XmaI to generate cohesive ends, and reisolatedfrom an agarose gel.

Plasmid pAK102 (A Y Kim and H P Blaschek, 1993, J. Bacteriol. 175:3838-43) was constructed by ligation of HindIII-linearized plasmid pUC19and a 2.3-kb HindIII erythromycin resistance gene fragment from plasmidpVA677 (F L Macrina et. Al, 1980, J. Bacteriol. 143: 1425-1435). pAK102encodes resistance to ampicillin and erythromycin, and replicatesautonomously in E. coli but not in Clostridium species; thus inClostridium, pAK102 is a “suicide vector.” Plasmids of equivalentfunction could be prepared from common E. coli vectors and commonsources of the erythromycin resistance gene functional in Clostridium(Methods for General and Molecular Microbiology, 3rd edition, 2007, C.A. Reddy editor in chief, ASM Press; Clostridia, 1989, Nigel P. Mintonand David J. Clarke editors, Plenum Press). Plasmid pAK102 DNA ispurified from a transformed E. coli DH5alpha host that is routinelygrown under 50 μg/mL of ampicillin selection, using a Qiagen Qiaprep®kit. The pAK102 DNA is linearized by digestion with XmaI and thepurified internal fragment of the spoIVA gene is cloned into the vectorusing DNA ligase.

The ligation mixture is electroporated into E. coli DH5alpha andtransformants are recovered by growth on LB agar petri plates ascolonies that are resistant to 50-100 μg/mL of ampicillin. Thetransformants are screened to determine the size of the Clostridiumfragment inserted into the plasmid. To do this, colony PCR is performedusing the same primers that were used above, and PCR reaction productsare separated by electrophoresis on 1% to 1.5% agarose gels.Transformants that show only the expected fragment size, and notmultiples of that size, are selected for the next step and are labeled“pAK102/spoIVA”.

Plasmid pAK102/spoIVA DNA is purified from the chosen E. colitransformant, using a Qiagen Qiaprep® kit. The plasmid DNA is used totransform strain C. beijerinckii NCIMB 8052 by electroporation.Transformants are initially allowed to recover by growth in TGY mediumwithout antibiotic selection for 3 hours at 35° C., then spread onTGY-1.5% agar plate medium containing 25 μg/mL of erythromycin.Alternatively, erythromycin concentrations as low as 10 μg/mL might beconsidered for the initial selective plates. Following their initialrecovery, erythromycin resistant strains are propagated in the presenceof 10-40 μg/L of erythromycin. Because the pAK102 vector is incapable ofindependent replication in Clostridium species, transformants areexpected to retain antibiotic resistance by virtue of having integratedthe pAK102/spoIVA construct into the chromosome, at a site bounded bythe endpoints of the cloned spoIVA fragment. The proper insertion of theplasmid, and its position within the spoIVA gene is verified by DNAsequencing of spoIVA gene target region.

The resulting strains, which are mutants of C. beijerinckii NCIMB 8052having disrupted or impaired spoIVA function, are tested infermentations for solvent formation in P2 medium as in Example 1, exceptthat 10-25 μg/L of erythromycin is added to the fermentation medium forevery 24 hours of elapsed culture time. The preservation and routinepropagation of the spoIVA mutant strains in the lab, as well as otherstrains that may be defective in the formation of normal spores, mayrequire the making and use of frozen cultures of vegetative cells inmedium containing 15% glycerol, or 0.1% DMSO, or other cryoprotectives.Such methods are known to those who are skilled in the art (Methods forGeneral and Molecular Microbiology, 3rd edition, 2007, C. A. Reddy(editor in chief), ASM Press) and could be used if necessary to preventthe emergence of degenerated strains by excessive serial propagationover time.

In the general manner of this example, derivatives of NCIMB 8052, orBA101 or other solventogenic Clostridium species and strains, areconstructed having mutations in other genes that are targeted forvarious degrees of disrupted function; for instance mutants bearingdefective spoVB, sspA, manIIAB or manIIC genes or their close homologs,or where expression of the normal gene is driven by reduced-strengthpromoters. In the case of Clostridium species having activerestriction-modification systems, such as for example C. acetobutylicumATCC 824 and other strains, steps to overcome the transformation barrierimposed by the restriction systems are added to the above protocol.Typically these involve prior methylation of the transforming DNA byvarious in vitro DNA methylation reactions, or by propagation of theDNA/vector in hosts that methylate the DNA but do not restrict it.Procedures for such modification are common in the research literatureof solventogenic clostridia (Handbook on Clostridia, 2005, Peter Durre(editor), Taylor & Francis publisher).

Example 7 Construction of Solventogenic Clostridia Engineered forConstitutive Expression of the adh Gene at High Levels from aHeterologous Promoter

A derivative of Clostridium beijerinckii strain NCIMB 8052 or BA101 isconstructed whereby the NCIMB 8052 adh gene (SEQ ID NO: 1, Cbei_(—)2181of GenBank CP000721) is constitutively expressed at increased levels bya combination of transcription from the promoter of the ferredoxin geneof Clostridium pasteurianum ATCC 6013, and by gene amplification on areplicative multicopy plasmid.

Plasmid pMTL500E is a multicopy E. coli/Clostridium shuttle vector thatencodes erythromycin resistance and which is stably maintained inClostridium strains including C. beijerinckii 8052 (AM López-Contreras,et. al., 2001, Clostridium beijerinckii cells expressing Neocallimastixpatriciarum glycoside hydrolases show enhanced lichenan utilization andsolvent production, Appl Environ Microbiol. 67: 5127-33; A Y Kim, et.al., Heterologous expression of endo-beta-1,4-D-glucanase fromClostridium cellulovorans in Clostridium acetobutylicum ATCC 824following transformation of the engB gene, 1994, Appl Environ Microbiol.60: 337-40; Handbook on Clostridia, 2005, Peter Durre editor, Taylor &Francis publisher).

The promoter and ribosome binding site (RBS) from the ferredoxin gene(fd) from Clostridium pasteurianum ATCC 6013 (GenBank accession numberM11214) has been shown to be capable of driving the constitutiveexpression of heterologous genes to very high levels in multipleClostridium species, including C. beijerinckii strain NCIMB 8052; (M CGraves and J C Rabinowitz, 1986, In vivo and in vitro transcription ofthe Clostridium pasteurianum ferredoxin gene. Evidence for “extended”promoter elements in gram-positive organisms, J Biol. Chem. 1986 261:11409-15; Minton N P, et. al., 1995, Chemotherapeutic tumour targetingusing clostridial spores, FEMS Microbiol Rev. 17: 357-64; U.S. Pat. No.6,652,849 (2003)).

To begin, plasmid pMTL500E DNA is linearized with restrictionendonuclease XmaI. Alternatively, another restriction site within themultiple cloning site (MCS) of the vector could also be used, providedXmaI in the remainder of the example is also replaced by thatrestriction enzyme.

A DNA fragment carrying the fd promoter and RBS sequences is prepared byoligonucleotide synthesis using the published DNA sequence for the fdpromoter and RBS binding region (GenBank accession number M11214),starting at the 5′ end from the first base of the source sequence (−168relative to the fd gene start codon) but incorporating an XmaI siteupstream of that, and replacing the sequence “TTCATG” with “CATATG” (anNdeI site) where “ATG” is the ferredoxin gene start codon, andterminating at the 3′ end with any string of non-homologous bases.Alternatively an fd promoter/RBS fragment featuring the same subterminalrestriction sites could be prepared by PCR amplification fromClostridium pasteurianum ATCC 6013 chromosomal DNA template. Thecomplete adh gene from C. beijerinckii strain NCIMB 8052 chromosomal DNAtemplate is amplified by PCR using a forward primer that includes asubterminal NdeI site, wherein the “ATG” of the NdeI site is also theATG start codon for the adh gene, and where the reverse primer includesa subterminal XmaI site. It should be noted that in this example, and inExample 8 and other examples incorporating this promoter replacementtactic, that there are alternative restriction recognition sitesincorporating ATC sequences that could be chosen for thepromoter-RBS-gene fusion, for example restriction endonucleases Nb.BsrDIor BsrDI.

The synthesized fd promoter/RBS fragment and the PCR-ed adh genefragment are purified, then digested with NdeI and ligated together,creating a “fd promoter/RBS/adh gene” fragment having subterminal XmaIsites. This is digested with XmaI and ligated into the linearizedpMTL500E plasmid. The reaction products are used to transform E. coliDH5alpha. Ampicillin resistant colonies are selected and thetransformant colonies are screened by DNA sequencing to confirm thepresence of the correct “fd promoter-RBS-adh gene” insert. The newplasmid is purified from the E. coli transformant and is used toelectroporate C. beijerinckii strain NCIMB 8052 or BA101. Erythromycinresistant transformant colonies are recovered as in Example 6.

Alternatively, the plasmid pMTL500F, which already has the fd promotersequence positioned upstream of an MCS (page 141, Chapter 6, in TheClostridia and Biotechnology, 1993, D. R. Woods editor,Butterworth-Heinemann), could be adapted as the cloning vector for theadh gene provided that the details of the method preserve a functioningRBS for expression of the cloned adh gene.

The resulting strains express adh constitutively due to the use of theheterologous fd promoter, and due to gene amplification on the multicopyvector. The expression of adh in the new strains is confirmed to beconstitutive, and is quantitated by enzyme assay. The new strains aretested in fermentations for solvent formation as in Example 1, includingthe addition of erythromycin to the fermentation medium for every 24hours of elapsed culture time.

Other promoters for constitutive gene expression are known in the artand would be suitable for use in this example; for instance, the ptb(phophobutyl transferase) gene promoter from C. acetobutylicum has beenused to drive constitutive expression of the LacI in several Clostridiumspecies—sufficient to suppress the fd promoter when under control of theLacZ operator (J T Heap, et. al., 2007, The ClosTron: a universal geneknock-out system for the genus Clostridium, J Microbiol Methods 70:452-64). Consequently, if tuning of the level of expression of the adhgene or other cloned genes is required to achieve the best result, otherpromoters can be tried as a means of achieving that end.

If further tuning of the expression level of the cloned adh is found tobe required, the method of cloning the gene is repeated with minormodifications to the DNA sequence of the RBS site, so as to alter theefficiency of ribosome binding and the level of functional gene productin the cell. (See page 167, The Clostridia and Biotechnology, 1993, D.R. Woods editor, Butterworth-Heinemann).

The following shows the DNA sequence in the RBS region of the native fdand adh genes, where the upper-case letters are the start codons of thegenes and the Shine-Dalgarno sequences of the RBS region are underlined.Tuning of the expression level of the cloned genes is accomplished byaltering either the sequence in the underlined regions, and the spacingbetween those regions and the ATG start codon.

adh ttttaggaggaa atattt ATG (SEQ ID NO: 20) fd tttaaggaggtgtatttttcATG(SEQ ID NO: 21) fd-adh tttaaggaggtgtatttcatATG SEQ ID NO: 22) (new)

In the general manner of this example, derivatives of C. beijerinckiistrain NCIMB 8052, or BA101 or other solventogenic Clostridium speciesand strains, are constructed having an increased level of expression, orconstitutive expression of other genes and their homologs, for instancethe bcd, buk, cheA, cheC and cheD genes. In the case of Clostridiumspecies having active restriction-modification systems, such as forexample C. acetobutylicum ATCC 824 and other strains, steps to overcomethe transformation barrier imposed by the restriction systems are addedto the above protocol as in example 6.

Example 8 Construction of Solventogenic Clostridia Engineered forConstitutive Expression of the adh Gene in Single Copy Number from aHeterologous Promoter

The methods of Example 6 and Example 7 can be combined and modified toachieve constitutive expression of the adh gene, at a level that islower than expression from a multicopy plasmid. This is achieved byintegrating the fd promoter-RBS-adh gene construct into the chromosomeof the Clostridium host. The expression level of the adh gene may behigher than the untransformed parent strain, or it may be lower than theuntransformed parent strain, depending upon the native level ofexpression of the adh gene in the untransformed strain, and uponmodifications to the fd promoter and RBS sequences of the engineeredstrain.

DNA of plasmid pAK102 DNA is prepared and linearized by digestion withXmaI as in Example 6.

A DNA fragment carrying the fd promoter and RBS sequences, engineered atthe ATG start codon to contain an NdeI site, is constructed as inExample 7.

A fragment of the adh gene from C. beijerinckii strain NCIMB 8052 (SEQID NO: 1, Cbei_(—)2181 of GenBank CP000721), consisting of the 5′one-third to one-half of the gene, is generated by PCR amplificationfrom chromosomal DNA, incorporating the 5′ NdeI site and 3′ XmaI site asin Example 7.

The fd-RBS fragment is ligated to the adh fragment at their NdeI sites,and then the fd-RBS-adh fragment is inserted by ligation into the XmaIsite of plasmid pAK102. The new plasmid construct is recovered andverified, and then electroporated into Clostridium beijerinckii NCIMB8052 or BA101 hosts and selected by erythromycin resistance as inExample 6. The resulting erythromycin resistant transformants aresingle-cross-over products between the cloned adh 5′ fragment on theplasmid, and the adh gene on the chromosome. The structure of theexpected construct, in order from 5′ to 3′ of the top strand of thegenome sequence, would be as shown below.

5′—partial adh gene—pAK102 vector—fd promoter—RBS—complete adh gene—3′

The erythromycin resistant transformants are checked by DNA sequencingto verify the expected structure.

The isolated new strains are maintained under erythromycin selection toprevent reversion by homologous crossing-out of the plasmid. The strainsare assayed for constitutive expression of adh enzyme, and for levels ofsolvent and acid formation in batch fermentation experiments. Due to itspresence in single copy number, the level of expression of adh would beexpected to be less than the strains of Example 7. As in example 7,further tuning of cellular levels of the Adh enzyme could beaccomplished by varying the constitutive promoter that is used (forexample, ptb) or by changing the sequence of the RBS region of theconstruct.

In the general manner of this example, derivatives of Clostridiumbeijerinckii NCIMB 8052, or BA101 or other solventogenic Clostridiumspecies and strains, are constructed having various levels ofconstitutive expression of other genes and their homologs, for instancethe bcd, buk, cheA, cheC and cheD genes. In the case of Clostridiumspecies having active restriction-modification systems, such as forexample C. acetobutylicum ATCC 824 and other strains, steps to overcomethe transformation barrier imposed by the restriction systems are addedto the above protocol as in example 6.

Example 9 Construction of Solventogenic Clostridia Engineered forReduced Expression of the sspA Gene Relative to the Untransformed Strain

Constitutive expression from the heterologous fd promoter, driving theexpression of a single copy of a gene as taught in Example 8, can bemodified to adjust the level of expression of the engineered gene. Suchmodification also could be in the direction of lowered expressionrelative to the untransformed host. This is advantageous in the instancewhere reduced gene expression is beneficial to solvent formation, butwhere complete elimination of gene expression produces undesirableeffects.

By introducing changes to the DNA sequence of the fd promoter, the levelof transcription of the gene is reduced leading to a reduction in mRNAlevels for the gene in the cell and lower levels of functional geneproduct. By altering the DNA sequence corresponding to the RBS and thespacing between the RBS and the ATG start codon of the gene, the levelof translation of the mRNA can be reduced, also leading to accumulationof less functional gene product in the cell. A combination of the mRNAreduction and translation reduction could lead any degree of reductionof gene expression without producing a full “knockout” affect.

DNA of plasmid pAK102 DNA is prepared and linearized by digestion withXmaI as in Example 6.

The 5′ one-half of the sspA gene from strain Clostridium beijerinckiiNCIMB 8052 (SEQ ID NO: 11, Cbei_(—)3080 of GenBank CP000721), isPCR-amplified from chromosomal DNA template, using a primer design thatincorporates a 5′ NdeI site and a 3′ XmaI site as in Example 7. Beingthat sspA is a short gene (210 bases), if suitable primers cannot befound, then a ClaI restriction site that exists near the middle of thegene is used to cleave the PCR amplification product and the 5′ half ofthe sspA gene is purified from an agarose gel.

A DNA fragment carrying the fd promoter and RBS sequences, engineered atthe ATG start codon to contain an NdeI site, is synthesized as inExample 7, including the creation of the 5′ XmaI and 3′ NdeI sites,except that instead of a single DNA sequence, a collection ofoligonucleotide species is produced having various nucleotide basechanges in the fd promoter and RBS sites.

The fd promoter of C. pasteurianum ATCC 6013 (GenBank M11214) has beencharacterized. It displays “minus-10” and “minus-35” sequences that arenot unlike those described for normal promoters of other gram-positivebacteria (M C Graves and J C Rabinowitz, 1986, J Biol. Chem. 1986 261:11409-15; page 287, The Clostridia and Biotechnology, 1993, D. R. Woodseditor, Butterworth-Heinemann). In particular, base changes introducedin the regions of minus-75 to minus-67, and minus-57 to minus-46relative to the ATG start codon of the fd gene could impact promoterstrength. Changes made to the RBS site at bases minus-17 to minus-11alter the efficiency of translation of mRNA to protein. These bases areunderlined in the DNA sequence below, which shows the fd promoter andRBS region of the oligonucleotide to be synthesized (the “atg” startcodon is shown in lower-case). By introducing one or several differentchanges in the underlined regions in the sequence of each fd-RBS DNAoligo that is synthesized, a mixture of oligonucleotidess bearingdifferent mutations in the region is produced.

(SEQ ID NO: 23) 5′_TTTAAAAAGTTTAAAAACATGATACAATAAGTTATGGTAAACTTATGATTAAAATTTTAAGGAGGTGTATTTCATatg_3′

The mixture of synthesized fd-RBS fragments bearing the differentmutations is ligated to the sspA fragment at their NdeI sites, and thenthe fd-RBS-sspA fragment is ligated into the XmaI site of plasmidpAK102. In the case of using ClaI to generate the sspA fragment, a bluntend ligation is done to close the plasmid. The new plasmid construct isrecovered and verified, and then electroporated into Clostridiumbeijerinckii NCIMB 8052 or BA101 hosts and selected by erythromycinresistance as in Example 6. The resulting erythromycin resistanttransformants are single-cross-over products between the cloned sspA 5′fragment on the plasmid, and the sspA gene on the chromosome. Theisolated new strains are maintained under erythromycin selection toprevent reversion by homologous crossing-out of the plasmid. As alludedto in Example 6, maintenance of the culture using techniques other thanspore propagation, such as frozen glycerol stocks of vegetative cells,might be necessary for some isolates.

The total collection of erythromycin-resistant isolates would comprise acollection of strains showing varying levels of expression of the sspAgene. The isolates are screened in fermentations for their ability toproduce more solvent or produce solvent more efficiently, or faster, asin Example 6. Candidates that show improved solvent forming propertiesor other desirable phenotypes are further characterized to determine thelocation of the inserted DNA in the chromosome, and the extent ofexpression of the sspA gene at both the transcriptional level (abundanceof mRNA) and translational level (abundance of SspA protein), and tocharacterize the sporulation and morphological properties of the newstrains.

In the general manner of this example, derivatives of Clostridiumbeijerinckii NCIMB 8052, or BA101 or other solventogenic Clostridiumspecies and strains, are constructed having a reduced level ofexpression of genes that are targeted for various degrees of reduction;for instance mutants showing reduced expression of spoIVA, spoVB,manIIAB or manIIC genes or their homologs. In the case of Clostridiumspecies having active restriction-modification systems, such as forexample C. acetobutylicum ATCC 824 and other strains, steps to overcomethe transformation barrier imposed by the restriction systems are addedto the above protocol as in example 6.

Example 10 Construction of Solventogenic Clostridia Engineered forInducible Expression of the bcd Gene

Plasmid pMTL5401F is a Clostridium/E. coli shuttle vector designed forinducible expression of cloned genes (JT Heap, et. al., 2007, TheClosTron: a universal gene knock-out system for the genus Clostridium, JMicrobiol Methods.: 452-64). For the purpose of this example itsessential elements are the ferredoxin gene fd promoter fused to theoperator of the lacZ operon (the promoter/operator combination is called“fac”), the lacI repressor gene under the control of the C.acetobutylicum ptb gene promoter, plasmid replication functions for E.coli and Clostridium hosts, and ampicillin and erythromycin resistancegenes for selection in E. coli and Clostridium hosts. In this system theLacd gene product represses transcription initiation at the fd promoterdue to the close proximity of the lac operator to the fd promoter. Inthe presence of the lactose analog IPTG(isopropyl-beta-D-thiogalactopyranoside), the LacI repressor fails tobind its operator and the fd promoter can then function. In this system,genes cloned downstream of the plasmid fac promoter/operator arerepressed until IPTG is added to the system, at which time the promoteris induced and the gene is expressed.

Plasmid pMTL5401F can be used for the inducible expression of the bcdgene (SEQ ID NO:2, Cbei_(—)2035 from GenBank CP000721). To do this a DNAfragment bearing the full-length bcd gene and including about 25 basesupstream of the bcd gene (to include the gene's RBS site, but no more),and having terminating restriction sites to control the length of DNAupstream and downstream of the gene, is prepared by PCR amplificationfrom C. beijerinckii strain NCIMB 8052 or strain BA101 chromosomal DNAtemplate. This fragment is then inserted into the linearized pMTL5401Fvector so as to bring the bcd gene and its RBS under the control of thefac promoter. Plasmid clones having the proper structure are thenrecovered and confirmed as in Example 7, and are labeled plasmid“pfac-bcd.”

C. beijerinckii strain NCIMB 8052 or BA101 is then transformed withpfac-bcd by electroporation and erythromycin resistant colonies areselected as in the other examples, and are maintained under erythromycinselection. Transformants are verified by DNA sequencing and then testedfor levels of bcd enzyme expression, and for solvent production in batchfermentations at various timepoints before and after induction of bcdgene expression by addition of IPTG to the culture. IPTG could be triedin the concentration range of 0.5 mM to 2 mM, but higher concentrationscould be tried if required.

As an alternative to the LacI/lacZ operator system, other induciblepromoter/operator systems for use in Clostridium species have also beendescribed and shown to function, for instance the adaptation of thexylose-inducible system from Staphylococcus xylosus for use in C.acetobutylicum (L Girbal, et. al., 2003, Development of a sensitive geneexpression reporter system and an inducible promoter-repressor systemfor Clostridium acetobutylicum, Appl Environ Microbiol.: 4985-8). To usethis system the xylA promoter-operator sequence is PCR amplified fromchromosomal DNA of S. xylosus strains DSM 20267. This could be clonedinto an appropriate vector, such as pMTL500E, or low-copy numberderivatives of the same replicon such as pMTL502E (page 45, Handbook onClostridia, 2005, Peter Durre editor, Taylor & Francis publisher) andused for xylose-inducible expression of cloned genes for solventproduction.

Alternatively, gene expression microarrays could be used to searchentire Clostridium genomes for promoters matching certain desiredexpression characteristics, including constitutive promoters, promotersof various strength for low-level, intermediate-level or high-levelexpression of genes, promoters responding to specific external factorssuch as chemical compounds that are added or that are present infermentation substrates, or promoters that follow certain desirabletemporal patterns of transcription initiation in the specificfermentation process that is being developed. To accomplish this,high-density microarrays representing entire genomes at high resolutionwould be prepared; for example arrays supplied by Roche NimbleGen, Inc.could be used. Messenger RNA to be amplified for final interrogation ofthe arrays would be isolated from cultures of Clostridium beijerinckiiNCIMB 8052 or BA101, or other Clostridium strains, under under multipledifferent conditions, the exact conditions depending on thepromoter-control objectives of the work. A time-course of the culturecould be used to discover promoters that show a temporal pattern ofactivity. Promoters that respond to specific added inducers, for examplexylose or arabinose, or furfual or HMF, etc., could be discovered bycomparing samples prepared before and after addition of thosesubstances. Constitutive promoters would be those that show relativelylittle change in activity in time-course experiments or in response toother challenges. The specific promoters of interest would be discoveredby the pattern of expression of the genes downstream of the promoters;in other words, one would analyze the microarray data to find specificgenes which expression reflects the desired patterns, then clone regionsupstream of those genes, or operons in the case of apparentco-transcription of contiguous genes, to discover the exact promoterthat displays the wanted characteristics.

In the general manner of this example, derivatives of C. beijerinckiistrain NCIMB 8052, or BA101 or other solventogenic Clostridium speciesand strains, are constructed having inducible expression of other genesand their homologs, for instance the adh, buk, cheA, cheC and cheDgenes. In the case of Clostridium species having activerestriction-modification systems, such as for example C. acetobutylicumATCC 824 and other strains, steps to overcome the transformation barrierimposed by the restriction systems are added to the above protocol as inexample 6.

Example 11 Construction of E. coli Strains Engineered to Express the adhGene from a Solventogenic Clostridium

Strains of E. coli are constructed that constitutively express the adhgene of C. beijerinckii strain NICMB 8052 from a strong constitutivepromoter. The strains are constructed by insertion of an E. colipromoter-Clostridium adh gene construct into the lacZ gene in thechromosome of E. coli, from a linear DNA fragment, by double crossoverrecombination into lacZ.

The Ptac and Ptrc promoters are constitutive synthetic promoters thatare often used for engineered expression of genes in E. coli (Herman A.De Boer, et al., The tac promoter: a functional hybrid derived from thetrp and lac promoters. Proc. Natl. Acad. Sci. 1983).

The adh gene (SEQ ID NO:1, Cbei_(—)2181 of GenBank CP000721) isamplified by PCR using chromosomal DNA from C. beijerinckii NCIMB 8052as template. The forward PCR primer is designed so as to incorporate thePtac promoter or the Ptrc promoter sequence and the lacZ ribosomebinding site, properly positioned in relation to the ATG start codon ofthe Clostridium adh gene to support expression of adh in E. coli. Thereverse primer is designed with a terminal HindIII restriction site tofacilitating its subsequent ligation to a tetracycline resistance genefragment (Tet^(R)) from pBR322 or a related vector.

A DNA fragment bearing the HindIII site and Tet^(R) gene and its nativepromoter is prepared by PCR amplification from a suitable vector, suchas pBR322 for example.

The Ptac-adh and Tet^(R) fragments are ligated together at their HindIIIsites, yielding a linear DNA fragment carrying the Tet^(R) gene and theadh gene, with the genes oriented for divergent transcription. TheTet^(R)-Ptac-adh or Tet^(R)-Ptrc-adh fragment is ligated into a pGEM-Tvector (Promega Corporation), disrupting the lacZ sequence of thatvector.

Using a Ptac promoter construct as an example, the pGEM-TlacZ::Ptac-adh-Tet^(R) plasmid is then linearized and electroporatedinto an E. coli recB recC sbcB host, which supports transformation andrecombination with linear DNA molecules (Winans, S. C., Elledge, S. J.,Krueger, J. H. & Walker, G. C., 1985, J. Bacteriol. 161: 1219-1221). Adouble crossover recombination event between the linearized plasmid andthe lacZ gene of the E. coli chromosome results in insertionalinactivation of the host lacZ gene, and a Tet^(R) lacZ phenotype fortransformants. Stable transformants are selected with tetracycyline, andtested for the lacZ phenotype, and for insertion of the expectedstructure into the chromosome by DNA sequencing.

In the general manner of this example, other solvent pathway genes fromvarious Clostridium species and strains, for instance the bcd, buk,cheA, cheC and cheD genes, could be cloned and expressed in E. colihosts.

All publications and patent applications cited in this specification areherein incorporated by reference as if each individual publication orpatent application were specifically and individually indicated to beincorporated by reference.

Although the foregoing invention has been described in some detail byway of illustration and example for purposes of clarity ofunderstanding, it will be readily apparent to those of ordinary skill inthe art in light of the teachings of this invention that certain changesand modifications may be made thereto without departing from the spiritor scope of the appended claims.

1. A first recombinant solventogenic organism comprising an alteredexpression of at least one gene involved in a solvent production pathwayrelative to the expression in the first organism strain prior to itstransformation, wherein the expression of the gene is altered in acorresponding manner in a hyper-butanol producing strain of a secondorganism, and further wherein said hyper-butanol producing strain of thesecond organism produces butanol more efficiently than a second organismstrain prior to its transformation.
 2. The recombinant solventogenicorganism of claim 1, wherein the second organism is a Clostridium sp. 3.The recombinant solventogenic organism of claim 2 wherein thehyper-butanol producing strain of the second organism is Clostridiumbeijernickii BA101.
 4. The recombinant solventogenic organism of claim1, wherein the altered expression of the gene is an increase inexpression of the gene.
 5. The recombinant solventogenic organism ofclaim 1, wherein the altered expression of the gene is a decrease inexpression of the gene.
 6. The recombinant solventogenic organism ofclaim 1, wherein the gene is selected from a gene involved in a pathwayselected from the group consisting of solventogenesis, chemotaxis, sporeformation and sugar transport.
 7. The recombinant solventogenic organismof claim 1, wherein the first and second organisms are the same species.8. The recombinant solventogenic organism of claim 1, comprisingincreased expression of a gene selected from the group consisting ofAdh, Bcd, and Buk, a homolog thereof, or a variant thereof, relative tothe organism strain prior to its transformation.
 9. The recombinantsolventogenic organism of claim 8, wherein the gene comprises anucleotide sequence having at least 80% homology to the sequenceselected from the group consisting of Adh (SEQ ID NO: 1), Bcd (SEQ IDNO: 2), and Buk (SEQ ID NO: 3) or complements thereof.
 10. Therecombinant solventogenic organism of claim 9, wherein the genecomprises a sequence at least 80% homologous to SEQ ID NO: 1 orcomplement thereof.
 11. The recombinant solventogenic organism of claim10, wherein the gene comprises a sequence of SEQ ID NO: 14 or complementthereof.
 12. The recombinant solventogenic organism of claim 10, whereinthe gene encodes a protein comprising a sequence of SEQ ID NO: 15 orcomplement thereof.
 13. The recombinant solventogenic organism of claim10, wherein the gene is an alcohol dehydrogenase.
 14. The recombinantsolventogenic organism of claim 9, wherein the gene comprises a sequenceat least 80% homologous to SEQ ID NO: 2 or complement thereof.
 15. Therecombinant solventogenic organism of claim 14, wherein the genecomprises a sequence of SEQ ID NO: 12 or complement thereof.
 16. Therecombinant solventogenic organism of claim 14, wherein the gene encodesa protein comprising a sequence of SEQ ID NO: 13 or complement thereof.17. The recombinant solventogenic organism of claim 14, wherein the geneis a butyryl-CoA dehydrogenase.
 18. The recombinant solventogenicorganism of claim 1, comprising increased expression of a gene selectedfrom the group consisting of CheA, CheC, and CheD, a homolog thereof, ora variant thereof, relative to the organism strain prior to itstransformation.
 19. The recombinant solventogenic organism of claim 1,comprising decreased expression of a gene selected from the groupconsisting of ManIIAB and ManIIC, a homolog thereof, or a variantthereof, relative to the organism strain prior to its transformation.20. The recombinant solventogenic organism of claim 1, comprisingdecreased expression of a gene selected from the group consisting ofSpoIVA, SpoVB, and SspA, a homolog thereof, or a variant thereof,relative to the organism strain prior to its transformation.
 21. Therecombinant solventogenic organism of claim 20, wherein the genecomprises a sequence at least 80% homologous to SEQ ID NO: 11 orcomplement thereof.
 22. The recombinant solventogenic organism of claim21, wherein the gene comprises a sequence of SEQ ID NO: 16 or complementthereof.
 23. The recombinant solventogenic organism of claim 21, whereinthe gene encodes a protein comprising a sequence of SEQ ID NO: 17 orcomplement thereof.
 24. The recombinant solventogenic organism of claim21, wherein the gene comprises a sequence of SEQ ID NO: 18 or complementthereof.
 25. The recombinant solventogenic organism of claim 21, whereinthe gene encodes a protein comprising a sequence of SEQ ID NO: 19 orcomplement thereof.
 26. The recombinant solventogenic organism of claim21, wherein the gene is a small acid-soluble spore protein.
 27. Therecombinant solventogenic organism of claim 1, wherein the gene is aheterologous nucleic acid.
 28. The recombinant solventogenic organism ofclaim 27, wherein the heterologous nucleic acid is controlled by aninducible promoter.
 29. The recombinant solventogenic organism of claim27, wherein the heterologous nucleic acid is controlled by aconstitutive promoter.
 30. The recombinant solventogenic organism ofclaim 27, wherein an mRNA transcribed from the heterologous nucleic acidaccumulates to a higher level relative to the organism strain prior totransformation.
 31. The recombinant solventogenic organism of claim 27,wherein a protein expressed from the heterologous nucleic acidaccumulates to a higher level relative to the organism strain prior toits transformation.
 32. The recombinant solventogenic organism of claim1, which is a yeast.
 33. The recombinant solventogenic organism of claim1, which is a bacteria.
 34. The recombinant solventogenic organism ofclaim 33, wherein the bacteria is an Escherichia or a Clostridium. 35.The recombinant solventogenic organism of claim 34, wherein the bacteriais a Clostridium beijerinckii.
 36. The recombinant solventogenicorganism of claim 34, wherein the bacteria is a recombinant Clostridiumbeijerinckii
 8052. 37. The recombinant solventogenic organism of claim34, wherein the bacteria is a recombinant Clostridium acetobutylicum.38. The recombinant solventogenic organism of claim 1 which iscellulolytic.
 39. The recombinant solventogenic organism of claim 1which is non-cellulolytic.
 40. The recombinant solventogenic organism ofclaim 1, wherein the gene has the DNA sequence of a gene fromClostridium beijernickii BA101.
 41. The recombinant solventogenicorganism of claim 1, wherein the gene encodes a protein comprising thesequence of a protein from Clostridium beijernickii BA101.
 42. Therecombinant solventogenic organism of claim 41, wherein the geneintroduced into the recombinant solventogenic organism is a heterologousnucleic acid from Clostridium beijernickii NCIMB
 8052. 43. Therecombinant solventogenic organism of claim 41, wherein the geneintroduced into the recombinant solventogenic organism is a heterologousnucleic acid from Clostridium beijernickii BA101.
 44. The recombinantsolventogenic organism of claim 1 which produces a solvent.
 45. Therecombinant solventogenic organism of claim 44 wherein the solvent isselected from the group consisting of butanol, ethanol and acetone. 46.The recombinant solventogenic organism of claim 44 which producesbutanol.
 47. A method of producing a solvent comprising culturing therecombinant solventogenic organism of claim
 1. 48. The method of claim47, wherein the solvent is selected from the group consisting ofbutanol, ethanol and acetone.
 49. The method of claim 47, wherein thesolvent is butanol.
 50. A method for making a recombinant solventogenicorganism comprising an altered expression level of at least one geneinvolved in a solvent production pathway relative to the expression ofthe gene in the organism strain prior to its transformation, the methodcomprising: identifying at least one gene related to production of asolvent comprising culturing cells in a medium comprising a substratefor solvent production, wherein expression level of the gene correlateswith production of solvent; and transforming an organism with a nucleicacid comprising the gene, wherein the nucleic acid is expressed in therecombinant solventogenic organism in a manner that causes therecombinant solventogenic organism to produce a solvent, wherein therecombinant solventogenic organism strain produces solvent moreefficiently than the organism strain prior to its transformation. 51.The method of claim 50 wherein the solvent is butanol.
 52. The method ofclaim 50, wherein said cultured cells are of a hyper-solvent producingstrain which produces butanol more efficiently than a wild type strain.53. The method claim 52 wherein, the cultured cells are Clostridiumbeijernickii BA101.
 54. The method of claim 50, further comprisingcomparing the expression level of the gene in the cultured cell to theexpression level of the gene in the corresponding wild type cell. 55.The method of claim 50, wherein the expression level is measured using amicroarray.
 56. The method of claim 50, further comprising transformingthe organism with a nucleic acid comprising a sequence at least 80%homologous to a wild type gene sequence.
 57. The method of claim 56,wherein the nucleic acid is operably linked to a promoter.
 58. Themethod of claim 50, wherein the gene expression is increased for genesselected from the group consisting of Adh, Bcd, Buk, CheA, CheC, andCheD, variants thereof and functional homologs thereof.
 59. The methodof claim 50, wherein the gene expression is decreased for genes selectedfrom the group consisting of ManIIAB, ManIIC, SpoIVA, SpoVB, and SspAmRNA, variants thereof and functional homologs thereof.
 60. The methodof claim 50, wherein the organism is a recombinant Clostridiumbeijerinckii.
 61. The method of claim 60, wherein the bacteria is arecombinant Clostridium beijerinckii NCIMB 8052.